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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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PhenoTips Resource Report Resource Website 10+ mentions |
PhenoTips (RRID:SCR_006340) | PhenoTips | software application, software resource | A software tool providing a Web interface and a database back-end for collecting clinical symptoms and physical findings observed in patients with genetic disorders. The main goals of this software are * To allow for collecting patient data in standard formats, enabling effortless data exchange and automated search in annotated gene and disease databases, and * To provide advanced functionalities and a friendly user interface that help reduce the clinician''''s workload, permitting seamless use of this application within the clinician''''s routine. PhenoTips uses the Human Phenotype Ontology (HPO) to express clinical phenotypes, and provides a friendly interface with error-tolerant, predictive search of phenotypic descriptions. PhenoTips closely mirrors clinician workflows: observations can be recorded directly during the patient encounter, and the interface is compatible with any device that runs a modern Web browser. The clinician can record demographic information, family history, medical history, various standard measurements, phenotypic abnormalities detected in the patient, pertinent indications that were not observed and that can be helpful for differential diagnosis, relevant images depicting manifestations of the patient''''s disorders, and additional notes for each of these categories. The software automatically plots growth curves, selects phenotypes reflecting abnormal measurements, instantly finds OMIM disorders matching the phenotypic description and suggests other symptoms to investigate in order to reach a more accurate diagnosis. | clinical symptom, physical finding, clinical, phenotype, demographic information, family history, medical history, standard measurement, indication, image, note, growth curve |
is related to: Human Phenotype Ontology is related to: OMIM has parent organization: University of Toronto; Ontario; Canada |
Genetic disorder | Free | nlx_152049 | SCR_006340 | SciCrunch Registry | PhenoTips: phenotyping made easy | 2026-10-31 12:21:10 | 24 | ||||||
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iBIOFind Resource Report Resource Website |
iBIOFind (RRID:SCR_001587) | iBIOFind | data or information resource, database, service resource, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. C#.NET 4.0 WPF / OWL / REST / JSON / SPARQL multi-threaded, parallel desktop application enables the construction of biomedical knowledge through PubMed, ScienceDirect, EndNote and NIH Grant repositories for tracking the work of medical researchers for ranking and recommendations. Users can crawl web sites, build latent semantic indices to generate literature searches for both Clinical Translation Science Award and non-CTSA institutions, examine publications, build Bayesian networks for neural correlates, gene to gene interactions, protein to protein interactions and as well drug treatment hypotheses. Furthermore, one can easily access potential researcher information, monitor and evolve their networks and search for possible collaborators and software tools for creating biomedical informatics products. The application is designed to work with the ModelMaker, R, Neural Maestro, Lucene, EndNote and MindGenius applications to improve the quality and quantity of medical research. iBIOFind interfaces with both eNeoTutor and ModelMaker 2013 Web Services Implementation in .NET for eNeoTutor to aid instructors to build neuroscience courses as well as rare diseases. Added: Rare Disease Explorer: The Visualization of Rare Disease, Gene and Protein Networks application module. Cinematics for the Image Finder from Yale. The ability to automatically generate and update websites for rare diseases. Cytoscape integration for the construction and visualization of pathways for Molecular targets of Model Organisms. Productivity metrics for medical researchers in rare diseases. iBIOFind 2013 database now includes over 150 medical schools in the US along with Clinical Translational Science Award Institutions for the generation of biomedical knowledge, biomedical informatics and Researcher Profiles. | workflow, model, prediction, research trend, rare disease, resource discovery, biomedicine, genomic, neural network, visualization, reporting, search engine, genetic, neural, clinical translation science award, biomedical resource, funding, gene, protein, neuron, collaborator, publication, trend, grant, funding opportunity, report |
is related to: ModelMaker is related to: Neural Maestro is related to: eNeoTutor is related to: Cytoscape is related to: Biomedical Resource Ontology is related to: PubMed has parent organization: The Cromwell Workshop |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_153829 | SCR_001587 | SciCrunch Registry | 2026-10-31 12:12:53 | 0 | ||||||||
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BIRD - Bio Info R and D Resource Report Resource Website 1+ mentions |
BIRD - Bio Info R and D (RRID:SCR_008010) | BIRD | data or information resource, organization portal, portal, topical portal | BIRD''s mission is to aid the progress of bioinformatics and promote creation of new biology, which has computational, deductive, predictive, and theoretical features. (most of this site is in Japanese) To carry out its responsibilities, BIRD: * Promotes appropriate development of bioinformatics research and development, such as what kinds of databases and analysis software should be developed and what kind of computer facilities are needed for that development. * Maintains the computer environment and network and functions as a funding agency to further promotion plans. * Develops basic databases: genome sequence database, protein 3D structure database, gene expression profile database, molecular interaction database, etc. * Conducts and coordinates integration, enhancement, and standardization of the basic databases. * Develops computing tools for analyzing various kinds of biological and experimental data, data mining from databases, computer simulation of living systems and so on. * Develops ontologies necessary for data and knowledge description of databases storing biological functions and integration of the basic databases. * Conducts and coordinates research and development of innovative and creative technologies and theories which move toward understanding life as an information system, especially approaches by collaboration of computer scientists and experimental scientists. * Provides computer facilities for developing databases and software and making them publicly available. * Sets up training courses for teaching utilization of databases and tools for novices in bioinformatics and sponsors scientific meetings. * Provides community space with high performance computing facilities where innovative ideas are cultivated by free discussion and "trial and error" with the computer in order to promote development of young scientists who will create new biological discoveries based on bioinfomatics and become leaders in the field. | data set | is listed by: 3DVC | nif-0000-09525 | SCR_008010 | SciCrunch Registry | Bio Info R and D, Bio Info RandD | 2026-10-31 12:14:48 | 2 | ||||||||
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Biositemaps Resource Report Resource Website 1+ mentions |
Biositemaps (RRID:SCR_001976) | Biositemaps | service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical data, tools and services (i.e., biomedical resources) over the Internet. All Institutions with an interest in biomedical research can publish a biositemap.rdf file on their Internet site. The technology, developed by the Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC), addresses (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site biositemap.rdf which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources. Each biositemap.rdf file is simply a list of controlled metadata about resources (software tools, databases, material resources) that your organization uses or believes are important to biomedical research. The key enabling technologies are the Information Model (IM) which is the list of metadata fields about each resource (resource_name, description, contact_person, resource_type,...) and the Biomedical Resource Ontology (BRO) which is a controlled terminology for the resource_typeand which is used to improve the sensitivity and specificity of web searches. Biositemaps blend the features of Sitemaps (enabling efficient web-content exploration) and RSS Feeds (a mechanism for wide and effective news dissemination). As a hybrid between Sitemaps and RSS feeds, the Biositemap infrastructure facilitates a decentralized, portable, extensible and computationally tractable generation and consumption of meta-data about existent, revised and new resources for biomedical computation. Web browsers, crawlers and robots can discover, accumulate, process, integrate and deliver Biositemaps content to (human or machine) users in a variety of graphical, tabular, computational formats. Biositemaps content allows such web browsers to pool resource-associated metadata from disparate and diverse sites and present it to the user in an integrated fashion. The Biositemaps protocol provides clues, information and directives for all Biositemap web harvesters that point to the existence and content of such biomedical resources at different sites. | broadcast, data federation, defined rdf schema, infrastructure, meta-data, rdf, retrieve, biomedical, biositemap, sitemap |
lists: Adaptively Sampled Particle Fluids lists: DicomWorks lists: MEDx lists: Medical Image Processing and Visualization lists: Surface-Based Atlases lists: RESNET lists: SurfRelax lists: FEATURE lists: Cardiovascular Model Repository lists: Simtk.org lists: ConTrack lists: Allopathfinder lists: Molecular Simulation Trajectories Archive of a Villin Variant lists: BioPortal lists: SumsDB lists: NeuronDB lists: BrainInfo lists: Protege lists: i2b2 Cross-Institutional Clinical Translational Research project lists: GeneChip Operating Software lists: Honig Lab lists: Proteomics Identifications (PRIDE) lists: ASAP: the Alternative Splicing Annotation Project lists: MiMI Plugin for Cytoscape lists: Substructure Index-based Approximate Graph Alignment lists: Proteome Commons Tranche repository lists: caTIES - Cancer Text Information Extraction System lists: REDCap lists: miniTUBA lists: Einstein-Montefiore ICTR Research Informatics Core lists: T-profiler lists: Stanford Translational Research Integrated Database Environment and Clinical Data Warehouse lists: GCG/SeqWeb lists: Solstice lists: California National Primate Research Center lists: BioGPS: The Gene Portal Hub lists: Blox lists: Subcellular Location Image Finder lists: PeptideAtlas lists: Clair library lists: Lyngby lists: SimTKCore lists: Velos lists: Ingenuity Pathway Analysis lists: Philips lists: Talktech lists: SUN Interface Engine lists: Quadramed - Medicus, Quantim lists: Wisconsin National Primate Research Center lists: i2b2 Research Data Warehouse lists: Merge Healthcare Incorporated lists: Clinical Trial Management Application lists: Cerner Millenium lists: Open Clinical Report Repository lists: Quovadx, Inc. lists: VectorValuedHistogramNormalizer lists: Morphometry BIRN lists: Talairach Daemon lists: LONI Visualization Tool lists: LONI Debabeler lists: LONI Pipeline Processing Environment lists: Brede Wiki lists: medInria lists: FreeSurfer lists: ITK-SNAP lists: VoxBo lists: Ensembl lists: MRIcron lists: Synchronized Histological Image Viewing Architecture lists: LONI ShapeViewer lists: LONI ShapeTools lists: FFT Library lists: NUTMEG lists: bioDBcore lists: Mutant Mouse Resource and Research Center lists: Brainscape lists: MindSeer lists: University of Southern California LONI Software lists: Statistics Online Computational Resource lists: NIH MRI Study of Normal Brain Development lists: Ontology Development and Information Extraction lists: Mindtouch DekiWiki lists: National Mesothelioma Virtual Bank lists: MGH-USC Human Connectome Project lists: Fusion ICA Toolbox lists: Biomedical Resource Ontology lists: Biomedical Informatics Research Network lists: 3D Slicer lists: Analysis of Functional NeuroImages lists: Automated Image Registration lists: TOADS-CRUISE Brain Segmentation Tools lists: BrainImage Software lists: Brede Toolbox lists: Whole Brain Catalog lists: Low Resolution Electromagnetic Tomography lists: Cambridge Brain Activation lists: ModelDB lists: fMRI Data Center lists: EEGLAB lists: 3DViewnix lists: MIPAV: Medical Image Processing and Visualization lists: NeuroLens lists: WFU PickAtlas lists: Protein Subcellular Location Image Database lists: STRIDE Virtual Biospecimen Bank lists: BrainVoyager is related to: Biomedical Resource Ontology is related to: Software Distribution Sets is related to: REX is related to: Rat Genome Database (RGD) has parent organization: National Centers for Biomedical Computing has parent organization: National Institutes of Health is parent organization of: Resource Discovery System |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10583 | SCR_001976 | SciCrunch Registry | 2026-10-31 12:21:00 | 1 | ||||||||
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RefGenome Resource Report Resource Website 1+ mentions |
RefGenome (RRID:SCR_004263) | RefGenome | data or information resource, data set | The GO Consortium coordinates an effort to maximize and optimize the GO annotation of a large and representative set of key genomes, known as ''reference genomes''. The goal of the Reference Genome Annotation project is to completely annotate twelve reference genomes so that those annotations may be used to effectively seed the automatic annotation efforts of other genomes. With more and more genomes being sequenced, we are in the middle of an explosion of genomic information. The limited resources to manually annotate the growing number of sequenced genomes imply that automatic annotation will be the method of choice for many groups. The Reference Genome project has two primary goals: to increase the depth and breadth of annotations for genes in each of the organisms in the project, and to create data sets and tools that enable other genome annotation efforts to infer GO annotations for homologous genes in their organisms. In addition, the project has several important incidental benefits, such as increasing annotation consistency across genome databases, and providing important improvements to the GO''s logical structure and biological content. All GO annotations from this project are included in the gene association files that each group submits to GO. Annotations can also be viewed using the GO search engine and browser AmiGO. Annotated families can be viewed with the homolog set browser. | has parent organization: Gene Ontology | PMID:19578431 | nlx_27840 | SCR_004263 | SciCrunch Registry | Reference Genome Annotation Project, Reference Genome Project | 2026-10-31 12:22:06 | 7 | ||||||||
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Cytoscape Resource Report Resource Website 10000+ mentions |
Cytoscape (RRID:SCR_003032) | data analysis software, data processing software, data visualization software, software application, software resource | Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. | biological, network, visualization, analysis, data, gene, pathway, molecular, interaction, FASEB list |
is used by: CytoSPADE is used by: HDBase is used by: DisGeNET is used by: categoryCompare lists: PEPPER is listed by: Debian is listed by: SoftCite is related to: PhosphoSitePlus: Protein Modification Site is related to: TRIP Database is related to: CoryneRegNet is related to: AltAnalyze - Alternative Splicing Analysis Tool is related to: MiMI Plugin for Cytoscape is related to: Network Data Exchange (NDEx) is related to: GeneMANIA is related to: DroID - Drosophila Interactions Database is related to: Network-based Prediction of Human Tissue-specific Metabolism is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: DaTo is related to: PiNGO is related to: iBIOFind is related to: cPath is related to: BiNGO: A Biological Networks Gene Ontology tool is related to: ClueGO is related to: RamiGO is related to: EGAN: Exploratory Gene Association Networks has parent organization: Institute for Systems Biology; Washington; USA has parent organization: University of California at San Diego; California; USA is parent organization of: JEPETTO has plug in: CluePedia Cytoscape plugin has plug in: CytoSPADE has plug in: EnrichmentMap has plug in: cytoHubba has plug in: iRegulon works with: NetCirChro works with: IMEx - The International Molecular Exchange Consortium works with: yFiles Layout Algorithms works with: RCy3 |
National Resource for Network Biology ; NCRR RR031228; NIGMS GM070743 |
PMID:21149340 PMID:14597658 |
Free, Available for download, Freely available | nif-0000-30404 | https://sources.debian.org/src/cytoscape/ | SCR_003032 | SciCrunch Registry | Complex Network Analysis Visualization, Cytoscape 2.6, Cytoscape 3.0 | 2026-10-31 12:13:16 | 25317 | |||||
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Google Code Resource Report Resource Website 100+ mentions |
Google Code (RRID:SCR_005786) | Google Code | software repository, software resource | Developer tools, APIs and resources. Search developers.google.com and code.google.com. | code, developer |
lists: Emotion Ontology lists: Porifera Ontology lists: Information Artifact Ontology lists: Mental Functioning Ontology lists: Beta Cell Genomics Ontology lists: Biological Collections Ontology lists: Chemical Methods Ontology lists: Chemical Information Ontology lists: Ontology for Genetic Interval lists: Ontology for Parasite LifeCycle lists: Ontology of Medically Related Social Entities lists: Population and Community Ontology lists: RNA Ontology lists: Vertebrate Taxonomy Ontology lists: Adverse Event Reporting Ontology lists: Neurobehavior Ontology lists: Ontology for General Medical Science lists: GHOSTM lists: nFuse lists: PD5 is parent organization of: GUARDD is parent organization of: APSampler is parent organization of: Cbrowse is parent organization of: SNAVI is parent organization of: TAPS is parent organization of: PyroHMMsnp is parent organization of: d2-tools is parent organization of: msbwt is parent organization of: DySC is parent organization of: BAMseek is parent organization of: GlycoWorkbench is parent organization of: Google Project Hosting is parent organization of: jmzIdentML API is parent organization of: jmzML is parent organization of: GenomicTools is parent organization of: tbrowse is parent organization of: PyroHMMvar is parent organization of: FR-HIT is parent organization of: PeptideShaker is parent organization of: ms lims is parent organization of: Gel2DE is parent organization of: ProRata is parent organization of: MoSDi is parent organization of: Gutentag is parent organization of: SASqPCR is parent organization of: MPprimer is parent organization of: BioCaster Ontology is parent organization of: PoPoolation2 is parent organization of: BMIQ is parent organization of: FadE is parent organization of: Bpipe is parent organization of: Snakemake is parent organization of: SNAPE-pooled is parent organization of: jmzTab is parent organization of: PoPoolation is parent organization of: PerM is parent organization of: tree editor is parent organization of: deStruct is parent organization of: PoPoolation TE is parent organization of: methylKit is parent organization of: SNPdat is parent organization of: CLEVER Toolkit is parent organization of: Clippers is parent organization of: Hydra is parent organization of: MiRPara is parent organization of: phantompeakqualtools is parent organization of: Knime4Bio is parent organization of: Bisulfighter is parent organization of: MOSAIK is parent organization of: SeqTrace is parent organization of: jMHC is parent organization of: BSMAP is parent organization of: PePr is parent organization of: SAAP-RRBS is parent organization of: SoftSearch is parent organization of: Autopack is parent organization of: CROP is parent organization of: eDMR is parent organization of: swDMR is parent organization of: peakrots is parent organization of: AmpliconNoise is parent organization of: HighSSR is parent organization of: ComB is parent organization of: Diplotyper is parent organization of: draw-sneakpeek is parent organization of: MutFinder is parent organization of: reseqtools is parent organization of: breseq is parent organization of: CNValidator is parent organization of: RRBSMAP is parent organization of: B-SOLANA is parent organization of: BatMeth is parent organization of: balony is parent organization of: ngs.plot is parent organization of: discovering-cse is parent organization of: SeqPipe is parent organization of: RseqFlow is parent organization of: orthAgogue is parent organization of: Gene ARMADA is parent organization of: MetExtract is parent organization of: jmzReader is parent organization of: PRIDE Converter 2 is parent organization of: Pride-asap is parent organization of: thermo-msf-parser is parent organization of: SearchGUI is parent organization of: XTandem Parser is parent organization of: Bpredictor is parent organization of: MOABS is parent organization of: CAMPways is parent organization of: compomics-utilities is parent organization of: DeNovoGUI is parent organization of: ProteoCloud is parent organization of: kruX is parent organization of: SlideSort-BPR is parent organization of: SPINAL is parent organization of: PSimScan is parent organization of: NetCoffee is parent organization of: CONDEX is parent organization of: ChiBE is parent organization of: Allim is parent organization of: Cell motility is parent organization of: GlycReSoft is parent organization of: GlycanBuilder is parent organization of: npstat is parent organization of: PoolHap is parent organization of: REDItools is parent organization of: iceLogo is parent organization of: AMS is parent organization of: MP-EST is parent organization of: HLAforest is parent organization of: LocalAli is parent organization of: genCAT is parent organization of: ECO is parent organization of: SobekCM is parent organization of: SimRare is parent organization of: PhenoMan is parent organization of: DistMap is parent organization of: PIPE-CLIP is parent organization of: CD-HIT is parent organization of: eagle-i research resource ontology is parent organization of: Neuropsychological testing ontology is parent organization of: Neurological disease ontology hosts: GenomeSmasher |
nlx_149265 | SCR_005786 | SciCrunch Registry | 2026-10-31 12:21:07 | 452 | |||||||||
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Bioconductor Resource Report Resource Website 10000+ mentions |
Bioconductor (RRID:SCR_006442) | software repository, software resource, software toolkit | Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data. | catalog, analysis, genomic, metadata, comprehension, statistical, data |
lists: MSstats lists: MetaCyto lists: MetaNeighbor lists: tximport lists: clusterProfiler lists: ropls lists: FlowSOM lists: scran lists: Rsubread lists: riboSeqR lists: Biostrings lists: ConsensusClusterPlus lists: DESeq2 lists: GenomicFeatures lists: affy lists: affydata lists: Genomic Ranges lists: Goseq lists: GAGE lists: CATALYST lists: Scmap lists: Scfind lists: GenomicRanges lists: org.Rn.eg.db lists: Extending Guilt by Association by Degree lists: ggtree lists: StructuralVariantAnnotation lists: scTHI lists: EnhancedVolcano lists: DEGreport lists: variancePartition lists: biomaRt lists: MSnbase lists: ReactomePA lists: SynergyFinder lists: CiteFuse lists: fgsea lists: GSVA lists: SimFFPE lists: FilterFFPE lists: PhenStat lists: ChIPseeker lists: AUCell lists: svaNUMT lists: KEGGgraph lists: epialleleR lists: microbiome lists: Orthology.eg.db lists: org.Hs.eg.db lists: ExperimentHub lists: combi is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: SoftCite is affiliated with: RnaSeqGeneEdgeRQL is related to: asSeq is related to: Gene Ontology is related to: CRCView is related to: R Project for Statistical Computing is related to: GEO2R is related to: LIMMA is related to: VisR is related to: edgeR is related to: IMEx - The International Molecular Exchange Consortium is related to: CATALYSTLite is related to: ascend is related to: minet has parent organization: Fred Hutchinson Cancer Center is parent organization of: ncdfFlow is parent organization of: GenomicRanges is parent organization of: ReadqPCR is parent organization of: flowCL is parent organization of: flowBin is parent organization of: CorMut is parent organization of: metaSeq is parent organization of: VariantAnnotation is parent organization of: ReQON is parent organization of: timecourse is parent organization of: RmiR.Hs.miRNA is parent organization of: AffyRNADegradation is parent organization of: ArrayExpress (R) is parent organization of: GEOquery is parent organization of: MIMOSA is parent organization of: HEM is parent organization of: CNTools is parent organization of: cn.FARMS is parent organization of: Clonality is parent organization of: TransView is parent organization of: pvac is parent organization of: QUALIFIER is parent organization of: flowStats is parent organization of: rTANDEM is parent organization of: flowFlowJo is parent organization of: iASeq is parent organization of: OLINgui is parent organization of: SigFuge is parent organization of: Rdisop is parent organization of: GeneExpressionSignature is parent organization of: iBMQ is parent organization of: TDARACNE is parent organization of: flowQ is parent organization of: FlipFlop is parent organization of: RmiR is parent organization of: bsseq is parent organization of: ExomePeak is parent organization of: flowWorkspace is parent organization of: massiR is parent organization of: rbsurv is parent organization of: GeneMeta is parent organization of: MergeMaid is parent organization of: categoryCompare is parent organization of: metahdep is parent organization of: snpStats: SnpMatrix and XSnpMatrix classes and methods is parent organization of: CNVtools is parent organization of: CGEN is parent organization of: RCASPAR is parent organization of: iterativeBMAsurv is parent organization of: multtest is parent organization of: globaltest is parent organization of: MinimumDistance is parent organization of: VegaMC is parent organization of: VanillaICE is parent organization of: SNPchip is parent organization of: SMAP is parent organization of: quantsmooth is parent organization of: mBPCR is parent organization of: ITALICS is parent organization of: GenoSet is parent organization of: exomeCopy is parent organization of: CGHregions is parent organization of: CGHbase is parent organization of: beadarraySNP is parent organization of: GLAD is parent organization of: methylMnM is parent organization of: methyAnalysis is parent organization of: ARRmNormalization is parent organization of: ChIPsim is parent organization of: yaqcaffy is parent organization of: wateRmelon is parent organization of: sRAP is parent organization of: spotSegmentation is parent organization of: SNM is parent organization of: SNAGEE is parent organization of: Simpleaffy is parent organization of: qcmetrics is parent organization of: MANOR is parent organization of: limmaGUI is parent organization of: ffpe is parent organization of: dyebias is parent organization of: DEXUS is parent organization of: BeadDataPackR is parent organization of: aroma.light is parent organization of: ArrayTools is parent organization of: beadarray is parent organization of: arrayQuality is parent organization of: arrayMvout is parent organization of: affyQCReport is parent organization of: affyPLM is parent organization of: AffyExpress is parent organization of: waveTiling is parent organization of: gprege is parent organization of: oneChannelGUI is parent organization of: LMGene is parent organization of: factDesign is parent organization of: pickgene is parent organization of: betr is parent organization of: SCAN.UPC is parent organization of: arrayQualityMetrics is parent organization of: CALIB is parent organization of: DEDS is parent organization of: Harshlight is parent organization of: MiChip is parent organization of: OCplus is parent organization of: bridge is parent organization of: fRMA is parent organization of: genArise is parent organization of: lapmix is parent organization of: maCorrPlot is parent organization of: maSigPro is parent organization of: MACAT is parent organization of: maigesPack is parent organization of: MDQC is parent organization of: metaArray is parent organization of: nnNorm is parent organization of: plgem is parent organization of: PVCA is parent organization of: RAMA is parent organization of: stepNorm is parent organization of: virtualArray is parent organization of: LPE is parent organization of: vsn is parent organization of: ACME is parent organization of: CoGAPS is parent organization of: flowFP is parent organization of: rMAT is parent organization of: SLqPCR is parent organization of: nondetects is parent organization of: unifiedWMWqPCR is parent organization of: sSeq is parent organization of: CNVrd2 is parent organization of: plateCore is parent organization of: RSVSim is parent organization of: TCC is parent organization of: CQN is parent organization of: COMPASS is parent organization of: flowClust is parent organization of: SPADE is parent organization of: OrderedList is parent organization of: SamSPECTRAL is parent organization of: flowUtils is parent organization of: RchyOptimyx is parent organization of: TEQC is parent organization of: flowType is parent organization of: ADaCGH2 is parent organization of: flowViz is parent organization of: flowTrans is parent organization of: flowQB is parent organization of: shinyTANDEM is parent organization of: flowPlots is parent organization of: flowPhyto is parent organization of: flowCore is parent organization of: flowMerge is parent organization of: flowMap is parent organization of: flowMeans is parent organization of: spliceR is parent organization of: flowMatch is parent organization of: flowFit is parent organization of: flowCyBar is parent organization of: BEAT is parent organization of: flowBeads is parent organization of: CAMERA - Collection of annotation related methods for mass spectrometry data is parent organization of: MBASED is parent organization of: MethylAid is parent organization of: sapFinder is parent organization of: Pathview is parent organization of: DSS is parent organization of: RMassBank is parent organization of: iontree is parent organization of: Basic4Cseq is parent organization of: BiGGR is parent organization of: mzR is parent organization of: PAPi is parent organization of: CGHnormaliter is parent organization of: Chimera is parent organization of: BRAIN is parent organization of: tweeDEseq is parent organization of: SurvComp is parent organization of: Triplex is parent organization of: OmicCircos is parent organization of: ggbio is parent organization of: HTqPCR is parent organization of: NormqPCR is parent organization of: ddCt is parent organization of: EasyqpcR is parent organization of: SWAN is parent organization of: PING is parent organization of: DMRforPairs is parent organization of: SeqGSEA is parent organization of: h5vc is parent organization of: deepSNV is parent organization of: RUVSeq is parent organization of: BHC is parent organization of: epigenomix is parent organization of: IRanges is parent organization of: GeneNetworkBuilder is parent organization of: MethylSeekR is parent organization of: SRAdb is parent organization of: casper is parent organization of: htSeqTools is parent organization of: ChIPXpress is parent organization of: methVisual is parent organization of: DeconRNASeq is parent organization of: EDASeq is parent organization of: RIPSeeker is parent organization of: ShortRead is parent organization of: seqbias is parent organization of: DEGseq is parent organization of: arrayMagic is parent organization of: easyRNASeq is parent organization of: DNAcopy is parent organization of: CRLMM is parent organization of: motifRG is parent organization of: MMDiff is parent organization of: MiRaGE is parent organization of: LVSmiRNA is parent organization of: ExiMiR is parent organization of: RPA is parent organization of: CexoR is parent organization of: lumi is parent organization of: baySeq is parent organization of: tRanslatome is parent organization of: DNaseR is parent organization of: DEXSeq is parent organization of: ChIPpeakAnno is parent organization of: inSilicoMerging is parent organization of: minfi is parent organization of: Methylumi is parent organization of: miRNApath is parent organization of: sva package is parent organization of: dmrFinder is parent organization of: rqubic is parent organization of: BicARE is parent organization of: iBBiG is parent organization of: eisa is parent organization of: ChAMP is parent organization of: cghMCR is parent organization of: Bioconductor mailing list is parent organization of: DiffBind is parent organization of: NarrowPeaks is parent organization of: CSAR is parent organization of: CSSP is parent organization of: TargetScore is parent organization of: snapCGH is parent organization of: iChip is parent organization of: TurboNorm is parent organization of: Ringo is parent organization of: RLMM is parent organization of: charm is parent organization of: BiSeq is parent organization of: MEDME is parent organization of: MEDIPS is parent organization of: BayesPeak is parent organization of: ChIPseqR is parent organization of: Rolexa is parent organization of: cn.mops is parent organization of: RankProd is parent organization of: phyloseq is parent organization of: HiTC is parent organization of: CancerMutationAnalysis is parent organization of: aCGH is parent organization of: Repitools is parent organization of: flowPeaks is parent organization of: Mfuzz is parent organization of: les is parent organization of: OLIN is parent organization of: affylmGUI is parent organization of: CYCLE is parent organization of: r3Cseq is parent organization of: Piano is parent organization of: RamiGO hosts: DESeq hosts: rGADEM hosts: PICS hosts: Jmosaics hosts: R453Plus1Toolbox hosts: BAC hosts: targetscan.Hs.eg.db hosts: Starr hosts: Qvalue hosts: topGO hosts: MmPalateMiRNA hosts: CGHcall hosts: EGSEA hosts: NOISeq |
Catt Family Foundation ; Dana Farber Cancer Institute ; NHGRI R33 HG002708 |
PMID:15461798 | Free, Freely available | OMICS_01759, nif-0000-10445 | SCR_006442 | SciCrunch Registry | 2026-10-31 12:21:09 | 24163 | |||||||
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ProbeExplorer Resource Report Resource Website |
ProbeExplorer (RRID:SCR_007116) | ProbeExplorer | analysis service resource, data analysis service, production service resource, service resource | Probe Explorer is an open access web-based bioinformatics application designed to show the association between microarray oligonucleotide probes and transcripts in the genomic context, but flexible enough to serve as a simplified genome and transcriptome browser. Coordinates and sequences of the genomic entities (loci, exons, transcripts), including vector graphics outputs, are provided for fifteen metazoa organisms and two yeasts. Alignment tools are used to built the associations between Affymetrix microarrays probe sequences and the transcriptomes (for human, mouse, rat and yeasts). Search by keywords is available and user searches and alignments on the genomes can also be done using any DNA or protein sequence query. Platform: Online tool | bioinformatics, microarray, oligonucleotide probe, transcript, genomic, genome, transcriptome, alignment, affymetrix, probe sequence, dna, protein, sequence, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of Salamanca; Salamanca; Spain |
Open unspecified license - Free for academic use | nlx_149275 | SCR_007116 | SciCrunch Registry | Probe Explorer | 2026-10-31 12:20:19 | 0 | |||||||
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Open PHACTS Resource Report Resource Website 10+ mentions |
Open PHACTS (RRID:SCR_005050) | OPS | consortium, data or information resource, database, organization portal, portal, software resource | Project that developed an open access discovery platform, called Open Pharmacological Space (OPS), via a semantic web approach, integrating pharmacological data from a variety of information resources and tools and services to question this integrated data to support pharmacological research. The project is based upon the assimilation of data already stored as triples, in the form subject-predicate-object. The software and data are available for download and local installation, under an open source and open access model. Tools and services are provided to query and visualize this data, and a sustainability plan will be in place, continuing the operation of the Open PHACTS Discovery Platform after the project funding ends. Throughout the project, a series of recommendations will be developed in conjunction with the community, building on open standards, to ensure wide applicability of the approaches used for integration of data. | drug, enzyme family, structure, receptor, target, ki, pathway, pharmacology, enzyme, small molecule, data mining, annotation, drug discovery, drug development, pharmacological profile, pharmacokinetic, admet data, biological target, chemical, linked data, rdf, nanopublication, platform, semantic technology, text mining, bioinformatics, cheminformatics, interoperability, chemistry, data provenance, compound, small molecule, semantic integration, drug discovery |
uses: CHEBI uses: ChemSpider uses: ConceptWiki uses: DrugBank uses: ENZYME uses: UniProt uses: Gene Ontology uses: WikiPathways is listed by: Consortia-pedia is listed by: FORCE11 is related to: Nanopub.org is related to: eTRIKS is related to: Janssen Research and Development is related to: Almirall is related to: ESTEVE is related to: Merck is related to: Pfizer Animal Genetics is related to: VU University; Amsterdam; Netherlands is related to: European Bioinformatics Institute is related to: Maastricht University; Maastricht; Netherlands is related to: University of Bonn; Bonn; Germany is related to: Royal Society of Chemistry is related to: Spanish National Cancer Research Center is related to: Netherlands Bioinformatics Centre is related to: SIB Swiss Institute of Bioinformatics is related to: Technical University of Denmark; Lyngby; Denmark is related to: University of Santiago de Compostela; Santiago de Compostela; Spain is related to: University of Vienna; Vienna; Austria is related to: University of Hamburg; Hamburg; Germany is related to: University of Manchester; Manchester; United Kingdom is related to: BioSolveIT is related to: ConnectedDiscovery is related to: OpenLink Software is related to: SciBite is related to: Open PHACTS Foundation has parent organization: University of Vienna; Vienna; Austria |
Innovative Medicines Initiative grant 115191; EFPIA ; Open PHACTS Foundation |
PMID:22683805 | Open unspecified license, Registration required, Non-commercial | r3d100011550, nlx_144033 | https://www.force11.org/node/4684, http://www.imi.europa.eu/content/open-phacts, https://doi.org/10.17616/R3T63F | SCR_005050 | SciCrunch Registry | Open PHACTS - Open Pharmacological Space, OpenPhacts.org, Open Pharmacological Space, Open Pharmacological Concepts Triple Store, OpenPHACTS, Open PHACTS: Open Pharmacological Space | 2026-10-31 12:13:56 | 11 | ||||
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canSAR Resource Report Resource Website 50+ mentions |
canSAR (RRID:SCR_006794) | canSAR | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | canSAR is an integrated database that brings together biological, chemical, pharmacological (and eventually clinical) data. Its goal is to integrate this data and make it accessible to cancer research scientists from multiple disciplines, in order to help with hypothesis generation in cancer research and support translational research. This cancer research and drug discovery resource was developed to utilize the growing publicly available biological annotation, chemical screening, RNA interference screening, expression, amplification and 3D structural data. Scientists can, in a single place, rapidly identify biological annotation of a target, its structural characterization, expression levels and protein interaction data, as well as suitable cell lines for experiments, potential tool compounds and similarity to known drug targets. canSAR has, from the outset, been completely use-case driven which has dramatically influenced the design of the back-end and the functionality provided through the interfaces. The Web interface provides flexible, multipoint entry into canSAR. This allows easy access to the multidisciplinary data within, including target and compound synopses, bioactivity views and expert tools for chemogenomic, expression and protein interaction network data. | molecular target, expression, cell line, compound, molecule, protein, structure, ligand, drug, 3d, genomics, 3d complex, bioactivity, protein affinity, cell line sensitivity, pathway, annotation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: BindingDB is related to: Gene Ontology has parent organization: Cancer Research UK |
Cancer | Cancer Research UK C309/A8274 | PMID:22013161 | CanSAR is freely available to all cancer researchers. By using canSAR you are agreeing to the Terms of Use, Https://cansar.icr.ac.uk/cansar/terms-of-use/ | biotools:cansar, nlx_149410 | https://bio.tools/cansar | SCR_006794 | SciCrunch Registry | 2026-10-31 12:14:38 | 56 | ||||
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Debian Resource Report Resource Website 50+ mentions |
Debian (RRID:SCR_006638) | Debian | data or information resource, database, software repository, software resource, source code | Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application. | operating system, software package, FASEB list |
lists: GUARDD lists: FACS lists: SNAVI lists: Fusion Analyser lists: GEOquery lists: MIMOSA lists: RNAcontext lists: AffyRNADegradation lists: Patchwork lists: GraBCas lists: GENIE3 lists: MODENT - A Tool For Reconstructing Gene Regulatory Networks lists: Megraft lists: PeptideProphet lists: VARiD lists: Flicker lists: ARACHNE lists: Quant lists: riboPicker lists: cn.FARMS lists: ProteinProphet lists: dbSTS lists: flowPeaks lists: SODOCK lists: PEPPER lists: POPBAM lists: Micro-Analyzer lists: MuTect lists: Mfuzz lists: PGS lists: TAPyR lists: ContEst lists: FPSAC lists: FlipFlop lists: SRMA lists: Pindel lists: PhenoFam lists: DSRC lists: SOAP lists: TriageTools lists: StringTie lists: SplitSeek lists: BLASR lists: Bowtie lists: Barrnap lists: MUSCLE lists: GimmeMotifs lists: massiR lists: CUDA-EC lists: Illuminator lists: SplicePlot lists: SLOPE lists: PARalyzer lists: VAAL lists: BreakSeq lists: ProGlycProt lists: OmicsOffice for NGS SeqSolve lists: TileQC lists: NGSUtils lists: QUAST lists: GenomicTools lists: piCALL lists: SNPchip lists: TALLYMER lists: SABER lists: wateRmelon lists: QualiMap lists: BFCounter lists: ADMIXTURE lists: OLIN lists: DEXUS lists: limmaGUI lists: KAnalyze lists: oneChannelGUI lists: BeadDataPackR lists: affylmGUI lists: SAMBLASTER lists: PyLOH lists: fRMA lists: CYCLE lists: FARMS lists: MACAT lists: GlyProt lists: YinOYang lists: Sequedex lists: DictyOGlyc lists: ToppCluster lists: Biocatalogue - The Life Science Web Services Registry lists: ProbRNA lists: HAPLOPAINTER lists: Chilibot: Gene and Protein relationships from MEDLINE lists: GERMLINE lists: FACTA+. lists: CisGenome lists: asSeq lists: unifiedWMWqPCR lists: HOMOZYGOSITYMAPPER lists: Prediction of Amyloid Structure Aggregation lists: InterMine lists: TANGO lists: CQN lists: MEME Suite - Motif-based sequence analysis tools lists: pRESTO lists: S-MART lists: PhosphoSitePlus: Protein Modification Site lists: myExperiment lists: DINDEL lists: Skylign lists: PEDIGRAPH lists: ADaCGH2 lists: CCAT lists: AnimalTFDB lists: TEMP lists: CanSNPer lists: Candida Genome Database lists: SamSPECTRAL lists: InteroPorc lists: MetaBase lists: Pecan lists: cisRED: cis-regulatory element lists: AffyPipe lists: SHORTY lists: BISC lists: Pathway Commons lists: Cake lists: SNVer lists: WebGeSTer DB lists: FlyFactorSurvey lists: ASPGD lists: TcoF lists: cpnDB: A Chaperonin Database lists: ZOOM lists: CAMERA - Collection of annotation related methods for mass spectrometry data lists: BEETL-fastq lists: NGSrich lists: ShotGun lists: Iterative Signature Algorithm lists: SBARS lists: SNPAAMapper lists: Autophagy Database lists: RUbioSeq lists: COSMIC - Catalogue Of Somatic Mutations In Cancer lists: EchoBASE lists: QualitySNPng lists: Pathview lists: pymzML lists: RopeBWT2 lists: ExomeDepth lists: NetPathMiner lists: leeHom lists: PurBayes lists: libCSAM lists: SuperPred: Drug classification and target prediction lists: HGNC lists: Coding Potential Calculator lists: T3DB lists: CPTRA lists: BioNumbers lists: GATE lists: ProRata lists: GreenPhylDB lists: BREAKDANCER lists: GeneFisher lists: tweeDEseq lists: HYDEN lists: Eukaryotic Linear Motif lists: Primer3Plus lists: MethylAid lists: Triplex lists: Distant Regulatory Elements lists: hot scan lists: MFEprimer lists: Proteome Analyst Specialized Subcellular Localization Server lists: mrsFAST lists: BioJS lists: FastSNP lists: Gene Set Enrichment Analysis lists: Pipeliner lists: ms lims lists: GenePattern lists: rBiopaxParser lists: QDNAseq lists: MutDB lists: Piano lists: NovelSeq lists: MAGE-TAB lists: Database of Interacting Proteins (DIP) lists: Weighted Gene Co-expression Network Analysis lists: Blood Group Antigen Gene Mutation Database lists: drFAST lists: pairheatmap lists: MiST - Microbial Signal Transduction database lists: AltAnalyze - Alternative Splicing Analysis Tool lists: SplicingCompass lists: deFuse lists: Assembly Based ReAligner lists: ggbio lists: miR-PREFeR lists: ALDEx2 lists: HTqPCR lists: NanoStringNorm lists: T-profiler lists: Snakemake lists: jmzTab lists: MIPgen lists: Bpipe lists: PoPoolation lists: L-Measure lists: MultiPhen lists: PheWAS R Package lists: InsertionMapper lists: Quantitative Enrichment of Sequence Tags lists: INMEX lists: Segway - a way to segment the genome lists: SeWeR - SEquence analysis using WEb Resources lists: TagDust lists: BSRD lists: DER Finder lists: Stem Cell Discovery Engine lists: Kdetrees lists: Tree and reticulogram REConstruction lists: BioPig lists: NCBI BioSystems Database lists: Distributed String Mining Framework lists: NEWT lists: PILGRM lists: Selectome: a Database of Positive Selection lists: SVMerge lists: Parseq lists: SVseq lists: Small Molecule Pathway Database lists: miRNAKey lists: DELLY lists: Apo and Holo structures DataBase lists: BioSample Database at EBI lists: MetaPhyler lists: MG-RAST lists: SLIQ lists: SOPRA lists: Information Hyperlinked Over Proteins lists: AmphoraNet lists: SINA lists: SSPACE lists: Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets lists: STING Report lists: G-BLASTN lists: RNA-eXpress lists: MethPipe lists: SoyBase lists: Strelka2 lists: RUM lists: SPOT - Biological prioritization after a SNP association study lists: VFS lists: PHAge Search Tool lists: MLTreeMap lists: SEECER lists: GeneTalk lists: ERANGE lists: rQuant lists: NCBO Annotator lists: ShoRAH lists: Yabi lists: ORMAN lists: FusionMap lists: CoPub lists: Scripture lists: SolexaQA lists: Kismeth lists: EMAGE Gene Expression Database lists: SAMStat lists: Knime4Bio lists: Bis-SNP lists: GobyWeb lists: Jellyfish lists: PRINSEQ lists: PASS lists: GSNAP lists: SOAPaligner/soap2 lists: MethylViewer lists: READSCAN lists: DistMap lists: MicrobesOnline lists: mrFAST lists: FLASH lists: TIGRFAMS lists: TMA Navigator lists: Bambino lists: TreQ lists: SeqMap lists: SeqTrace lists: TRANSFAC lists: GoFish lists: MethylomeDB lists: CLIPZ lists: SerbGO lists: ToppGene Suite lists: ngsTools lists: PePr lists: DMRforPairs lists: CharProtDB: Characterized Protein Database lists: Expression Profiler lists: SNPsandGO lists: GoSurfer lists: WEGO - Web Gene Ontology Annotation Plot lists: SOURCE lists: Stampy lists: DiseaseMeth lists: BLESS lists: GraphProt lists: GoPubMed lists: ccPDB - Compilation and Creation of datasets from PDB lists: Europe PubMed Central lists: Dr.VIS - Human Disease-Related Viral Integration Sites lists: DOMMINO - Database Of MacroMolecular INteractiOns lists: DBETH - Database for Bacterial ExoToxins for Humans lists: VirHostNet: Virus-Host Network lists: GWASdb lists: HFV Database lists: HotRegion - A Database of Cooperative Hotspots lists: eQuilibrator lists: FunTree lists: Cascade lists: 959 Nematode Genomes lists: ICEberg lists: IndelFR - Indel Flanking Region Database lists: IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature lists: ProRepeat lists: NRG-CING lists: InterEvol database lists: MMMDB - Mouse Multiple tissue Metabolome DataBase lists: Newtomics lists: MIPModDB lists: DistiLD - Diseases and Traits in LD lists: Polbase lists: UMD-BRCA1/ BRCA2 databases lists: ScerTF lists: VIRsiRNAdb lists: ProPortal lists: OGEE - Online GEne Essentiality database lists: RecountDB lists: PRED-GPCR lists: RNA CoSSMos lists: PRED-SIGNAL lists: SNPedia lists: SpliceDisease lists: HMM-TM lists: deepSNV lists: OMPdb lists: PRED-LIPO lists: VICUNA lists: Predictive Networks lists: COEUS lists: GeneTrail lists: epigenomix lists: ADGO lists: SRAdb lists: QCGWAS lists: Flycircuit lists: MouseBook lists: Immune Epitope Database and Analysis Resource (IEDB) lists: SitEx lists: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit lists: MSIsensor lists: TSSer lists: ATRHUNTER lists: Phytozome lists: Decombinator lists: ViralZone lists: COLT-Cancer lists: Gene Expression Database lists: BEDTools lists: waviCGH lists: Pseudomonas Genome Database lists: BIGpre lists: MyHits lists: CAPS Database lists: SpliceTrap lists: EagleView lists: IMGT/LIGM-DB lists: RIKEN integrated database of mammals lists: COHCAP lists: DARC - Database for Aligned Ribosomal Complexes lists: canSAR lists: GWAMA lists: AutismKB lists: zfishbook lists: PomBase lists: Myrna lists: PLEXdb - Plant Expression Database lists: RamiGO lists: PhenoM - Phenomics of yeast Mutants lists: IMGT/GENE-DB lists: HIstome: The Histone Infobase lists: SCOP: Structural Classification of Proteins lists: CuticleDB lists: agriGO lists: Expression Database in 4D lists: ESEfinder 3.0 lists: TriTrypDB lists: VIDA lists: Database of Arabidopsis Transcription Factors lists: Atlas of Genetics and Cytogenetics in Oncology and Haematology lists: AgBase lists: Hyper Cell Line Database lists: Midbody, Centrosome and Kinetochore lists: Chromosome 7 Annotation Project lists: MfunGD - MIPS Mouse Functional Genome Database lists: Taipan lists: VISTA Browser lists: T1DBase lists: lobSTR lists: VISTA Enhancer Browser lists: MEROPS lists: Gene Array Analyzer lists: Network Analysis, Visualization and Graphing TORonto lists: Candidate Genes to Inherited Diseases lists: Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) lists: eTBlast lists: hiPathDB - human integrated Pathway DB with facile visualization lists: MuSiC lists: miRNEST lists: QuasiRecomb lists: neXtProt lists: DNAtraffic lists: BeeBase lists: NetOGlyc lists: GenoTan lists: GMAP lists: LegumeIP lists: SeqBuster lists: elastix lists: iMir lists: WEBLOGO lists: MaCH-Admix lists: Pathema lists: SNPinfo Web Server lists: MOSCPHASER lists: NEBcutter lists: Atlas2 lists: FGDP lists: Velvet lists: HomSI lists: MicroSNiPer lists: MIRA lists: ALLPATHS-LG lists: CUPSAT lists: SVDetect lists: omiRas lists: CopySeq lists: MutSig lists: HapFABIA lists: DIANA-LncBase lists: MutationTaster lists: HMCan lists: Geneious lists: kmer-SVM lists: SICER lists: ZINBA lists: Pedimap lists: MAnorm lists: PlantTFcat lists: MethMarker lists: NPS lists: PeakRanger lists: SEAL lists: OligoArray lists: PSAR-Align lists: CEQer lists: CloudBurst lists: nucleR lists: RACE lists: Asterias lists: PatMaN lists: RobiNA lists: LitInspector lists: Btrim lists: ArrayAnalysis.org lists: CANGS lists: GeneStitch lists: ProDesign lists: JiffyNet lists: AlienTrimmer lists: GenoREAD lists: HSLPred lists: CancerResource lists: FABIA lists: PlnTFDB lists: easyRNASeq lists: OBI-Warp lists: PREDDIMER lists: ECHO lists: ICPL ESIQuant lists: PRIDE Converter 2 lists: SlideSort-BPR lists: COBRApy lists: MFPaQ lists: TopHat-Fusion lists: miRPlant lists: SNP ratio test lists: compomics-utilities lists: PLEK lists: multiplierz lists: Allim lists: ISDTool lists: NetCoffee lists: MToolBox lists: Scalpel lists: DNaseR lists: LocalAli lists: NAIL lists: iceLogo lists: GPU-Meta-Storms lists: AMS lists: rqubic lists: ANNOVAR lists: A5-miseq lists: PhosphoSiteAnalyzer lists: Cell motility lists: MethylCoder lists: CAZy- Carbohydrate Active Enzyme lists: CPFP lists: GENE-counter lists: PoolHap lists: LOCAS lists: CloudAligner lists: HeurAA lists: Mouse Genome Database lists: MitoBreak lists: PolyPhen: Polymorphism Phenotyping lists: GSA-SNP lists: featureCounts lists: Crossbow lists: CSAR lists: seqMINER lists: BEADS lists: IUPHAR/BPS Guide to Pharmacology lists: QuantiSNP lists: Cube-DB lists: Death Domain database lists: psRNATarget lists: DSAP lists: PlantNATsDB - Plant Natural Antisense Transcripts DataBase lists: GeneSigDB lists: MACS lists: NGSmethDB lists: GENSCAN lists: INCLUSive lists: MINAS - Metal Ions in Nucleic AcidS lists: Composition Profiler lists: NNcon lists: EGSEA lists: SCRATCH lists: Telescoper lists: Buccaneer lists: ProtTest lists: Morpheus lists: KAVIAR lists: DISEASES lists: SPEX2 lists: RAST Server lists: GeneWise lists: Crystallography and NMR System (CNS) lists: FATCAT lists: Membrane Protein Explorer lists: LTR_Finder lists: PALEOMIX lists: TISSUES lists: MetaMapR lists: primers4clades lists: MS-GF+ lists: PLAN2L lists: Off-Spotter lists: ProteomicsDB lists: CHiCAGO lists: SC3 lists: Bio-tradis lists: ApiDB CryptoDB lists: HISAT2 lists: PhyD3 lists: LoRDEC lists: Bamtools lists: ALTER lists: MultiQC lists: TFBS lists: EnrichmentMap lists: Poretools lists: Exonerate lists: 3D-footprint lists: Genesis lists: oligo lists: DISULFIND lists: Fastml lists: mentha lists: Oufti lists: eXpression2Kinases lists: IDEPI - IDentify EPItopes lists: SMAGEXP lists: ProCon - PROteomics CONversion lists: TRANSIT lists: DINIES lists: Splicing Express lists: FluxModeCalculator lists: Lifebit Deploit lists: ngsRelate lists: SARTools lists: OmicsNet lists: SPICE lists: Microscopy Image Browser lists: Thunder STORM lists: clusterProfiler lists: NetworkAnalyst lists: ANOCVA lists: Rsubread lists: Subread lists: ConsensusClusterPlus lists: CIBERSORT lists: FRETBursts lists: CCTOP lists: scran lists: ScaffMatch lists: Heatmapper lists: Goseq lists: PRSice lists: UMI-tools lists: Proovread lists: BinPacker lists: JAMM lists: CentroidFold lists: ComplexHeatmap lists: PatchDock lists: FastProject lists: ExPASy ABCD database lists: Gigwa lists: shinyGEO lists: GeSeq lists: EMBOSSMatcher lists: Geneshot lists: Mousebytes lists: trimAl lists: AmoebaDB lists: STRUCTURE lists: PASTEClassifier lists: NetPhos lists: HiC-Pro lists: SWISS-MODEL lists: Blood Exposome Database lists: HingeProt lists: ChiCMaxima lists: ProtParam Tool lists: GalaxyRefine lists: FlowCal lists: SpydrPick lists: R/qtl2 lists: Roary lists: SIGNOR lists: Protein Interactions Calculator lists: REDIportal lists: MaxAlign lists: Minimap2 lists: PrognoScan lists: GPS-SUMO lists: Signaling Pathways Project lists: ProSA-web lists: GalaxyWEB lists: iTOL lists: EpiModel lists: rVista lists: AlgPred lists: D-GENIES lists: Robetta lists: GOnet lists: E-CRISP lists: STAMP lists: Batch Web CD-Search Tool lists: aroma.light lists: Annotree lists: Database of Secondary Structure Assignments lists: Clustal Omega lists: DESeq lists: discoSnp lists: vcflib lists: Genome BioInformatics Research Lab - gff2ps lists: Primer3 lists: BioPerl lists: Rainbow lists: RNAhybrid lists: Clustal W2 lists: Apollo lists: IgBLAST lists: Ray lists: khmer lists: Stacks lists: Predictions for Entire Proteomes lists: DIALIGN lists: EBSeq lists: Minia lists: SAMtools/BCFtools lists: Artemis: Genome Browser and Annotation Tool lists: NCBI BLAST lists: biobambam lists: VICMpred lists: Staden Package lists: Bowtie 2 lists: RAxML lists: WHAM lists: VarScan lists: Bismark lists: ea-utils lists: HTSeq lists: Vienna RNA lists: Regulatory Sequence Analysis Tools lists: BitSeq lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: HilbertVis lists: BRIG lists: Unipro UGENE lists: GBrowse lists: Sickle lists: AmpliconNoise lists: FreeBayes lists: tRNAscan-SE lists: CD-HIT lists: SSAKE lists: MACH lists: Segemehl lists: BEAST lists: Pscan-ChIP lists: cutadapt lists: Oases lists: CGView lists: SOAPsnp lists: T-Coffee lists: Kalign lists: Circos lists: Trinity lists: Flexbar lists: SIFT lists: ProbCons lists: OpenMS lists: RSEM lists: Glimmer lists: GROMACS lists: CummeRbund lists: edgeR lists: DNAcopy lists: TopHat lists: SortMeRNA lists: LIMMA lists: AMOS lists: Cufflinks lists: Nanopolish lists: GMA lists: Prokka lists: phyloseq lists: SeqPrep lists: precrec lists: Atac lists: PAML lists: KisSplice lists: StoatyDive lists: IMGT-ONTOLOGY lists: KAT lists: SeaView lists: FastTree lists: Crux tandem mass spectrometry analysis software lists: rCASC lists: minet lists: becas lists: tximport lists: globaltest lists: CheckM lists: BLINK lists: mosdepth lists: bwtool lists: dcmqi lists: Pilon lists: ASHLAR lists: metagen lists: COPASI lists: BUSCO lists: bridge lists: TGS-GapCloser lists: NiftyPET lists: Blobtools lists: THESIAS lists: Fcirc lists: chimerascan lists: GLUE lists: SwiftOrtho lists: HaploReg lists: ScanITD lists: andi lists: metahdep lists: ImaGene lists: Jalview lists: MeroX lists: qrqc lists: BioNix lists: MiXCR lists: casper lists: libmgf lists: sleuth lists: imDEV lists: miRDB lists: yaqcaffy lists: NiftyFit lists: mlgt lists: SMARTdenovo lists: HH-suite lists: StatAlign lists: affy lists: shovill lists: Fiji lists: Racon lists: rbsurv lists: quantsmooth lists: tensorflow lists: seqbias lists: ngs.plot lists: bsseq lists: MGnify lists: dyebias lists: h5vc lists: ascat lists: Cuffdiff lists: mitopred lists: OrthoFinder lists: PIRATE lists: Bridger lists: Eoulsan lists: VEnCode lists: eTRIKS lists: fracridge lists: lumi lists: genomation lists: Hippocampome.org lists: SymPy lists: icy lists: GADMA lists: HaTSPiL lists: XL-mHG lists: ropls lists: scanpy lists: MethBase lists: sabre lists: plgem lists: MyGene.info lists: CRISPRcasIdentifier lists: biobakery lists: VETA lists: EpiEstim lists: HyPhy lists: ODAM lists: BISE lists: docker4seq lists: qcmetrics lists: Pavian lists: genehunter-imprinting lists: smashpp lists: NanoSim lists: SimVascular lists: BSA4Yeast lists: minfi lists: TDimpute lists: RepeatScout lists: neuroelectro lists: MRIcron lists: RepeatFiller lists: ShinyLearner lists: CRISPR-ERA lists: CRISPR-P lists: Warp lists: GEMINI lists: MAFFT lists: TransDecoder lists: Phenoscape lists: PhenoMeNal lists: les lists: Laniakea lists: CandiMeth lists: eisa lists: ProP Server lists: ggtree lists: scVelo lists: PathwayMatcher lists: charm lists: Telescope lists: skewer lists: multtest lists: Human Neocortical Neurosolver lists: beadarray lists: BioBERT lists: PlotTwist lists: GraphClust2 lists: METAREP lists: QIIME lists: halSynteny lists: scater lists: Galaxy scater lists: larvalign lists: iontree lists: VAPPER lists: GENCODE lists: Datanator lists: Bio2BEL lists: UALCAN lists: ffpe lists: MCScan lists: VisR lists: Metascape lists: GemSIM lists: EvidenceFinder lists: pepwheel lists: RDXplorer lists: bcbio-nextgen lists: OpenWorm lists: ActiveDriver lists: QuickNII lists: timecourse lists: Bionitio lists: ggplot2 lists: TCW lists: SPM lists: pvac lists: GeneMarkS-T lists: ascend lists: RatMine lists: CRISPRdirect lists: phantompeakqualtools lists: prank lists: refgenie lists: NanoPipe lists: vsn lists: PAFScaff lists: odMLtables lists: biospytial lists: NeuroChaT lists: clustergrammer lists: glycomedb lists: CLIP-Explorer lists: pheatmap lists: EnteroBase lists: GigaSOM.jl lists: bio.tools lists: SPP lists: lapmix lists: EHRtemporalVariability lists: HmtVar lists: SnpHub lists: Online Peri-Event Time Histogram for Open Ephys lists: NMRProcFlow lists: QGIS lists: Flye lists: kallisto lists: clipcrop lists: cn.mops lists: UniCarbKB lists: pickgene lists: PsyGeNET lists: seq-annot lists: PASA lists: ReadqPCR lists: breseq lists: e-Driver lists: sim4cc lists: PhylomeDB lists: fastqz lists: PerM lists: rnaQUAST lists: NCBI BioProject lists: PEMer lists: metabnorm lists: FusionCatcher lists: STAR lists: VCFtools lists: UniCarb-DB lists: NormqPCR lists: SnpEff lists: DecGPU lists: gprege lists: VirusMINT lists: nondetects lists: circlize lists: SAMTOOLS lists: Neuroscience Information Framework lists: Dali Server lists: IRanges lists: dbEST lists: Genomic Ranges lists: eProbalign lists: Cistrome lists: DIANA-mirPath lists: BpForms lists: GenomicFeatures lists: SOAPdenovo lists: BcForms lists: 4See lists: ABNER lists: A Classification of Mobile genetic Elements lists: Addgene lists: BadMedicine lists: ADMIXMAP lists: ADMIXTOOLS lists: ALCHEMY lists: AETIONOMY lists: ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters lists: ALBERT lists: ALOHOMORA lists: Alternate splicing gallery lists: Allele Frequencies in Worldwide Populations lists: AmpliconTagger lists: Molecular Dynamics Workflow (BioKepler) lists: ape lists: Alta-Cyclic lists: Assisted Model Building with Energy Refinement (AMBER) lists: Aroma.affymetrix lists: ANDES lists: ASSOCIATIONVIEWER lists: ArrayMiner lists: ASPEX lists: The Alternatve Splicing Database lists: AutoAssemblyD lists: AutoDock Vina lists: BAIT lists: BamView lists: Avogadro lists: ArrayPipe lists: Athena lists: BLAT lists: BARS lists: BayesEpiModels lists: BatMeth lists: BeetleBase lists: BBSeq lists: naiveBayesCall lists: BarraCUDA lists: BCBtoolkit lists: BioConda lists: BAR lists: BiG-SLiCE lists: SVM based method for predicting beta hairpin structures in proteins lists: betaVAEImputation lists: BiNGO: A Biological Networks Gene Ontology tool lists: Bioinformatics Toolkit lists: BioCarta Pathways lists: Biopieces lists: Bio++ lists: BioPlex lists: BioSimulations lists: BRAIN lists: BOMP: beta-barrel Outer Membrane protein Predictor lists: biomaRt lists: bioSyntax lists: Bionimbus lists: BioSimulators lists: bioRxiv lists: Breakpointer lists: CiLiQuant lists: BSVF lists: BS Seeker lists: Bs-Seeker2 lists: BWA lists: CARD lists: Canu lists: Cell Image Library (CIL) lists: BRB-ArrayTools lists: CATALYST lists: CATH: Protein Structure Classification lists: CAT lists: CEM lists: CASPAR lists: CHEBI lists: ChimeraSlayer lists: CATdb: a Complete Arabidopsis Transcriptome database lists: ChemSpider lists: Chipster lists: CCREL lists: cisTEM lists: circlncRNAnet lists: Centrifuge Classifier lists: Cancer Genome Anatomy Project lists: ChIPMunk lists: Chromas lists: CiteFuse lists: CRCView lists: ChiRA lists: ClinVar lists: ClinTrajAn lists: clustLasso lists: CleanEx lists: Clinotator lists: CNVer lists: ComiR lists: CODEHOP lists: ClustVis lists: Comparative Metatranscriptomics Workflow lists: CMap lists: CorMut lists: CNV-seq lists: Coot lists: CITE-seq-Count lists: CoCo lists: CopyDetective lists: Chromosome Scale Assembler lists: cortex lists: ConDeTri lists: CRISPy-web lists: CONTRA lists: CovalentDock Cloud lists: CUDASW++ lists: COGEME Phytopathogenic Fungi and Oomycete EST Database lists: DANPOS2 lists: DOGMA lists: CorrDrugTumorMSI lists: DAMBE lists: D-EE lists: CoryneRegNet lists: ΔG prediction server lists: DIAMOND lists: CYANA lists: Datasets2Tools lists: DEXSeq lists: DichroWeb lists: NCBI database of Genotypes and Phenotypes (dbGap) lists: DBTSS: Database of Transcriptional Start Sites lists: dbSNP lists: DiffBind lists: DETONATE lists: DiProGB lists: Descriptions of Plant Viruses lists: DIME lists: DicomTypeTranslator lists: CSDeconv lists: Dictyostelium discoideum genome database lists: DSK lists: DGIdb lists: DisProt - Database of Protein Disorder lists: DOMINE: Database of Protein Interactions lists: eDMR lists: ECLIPSE lists: Experimental Design Assistant lists: Dissect lists: Evolutionary Couplings Server lists: Enrichr lists: ensembldb lists: European Genome phenome Archive lists: EBCall lists: Ensembl Genomes lists: EMAN lists: ENIGMA lists: DISENTANGLER lists: Entrez Gene lists: Ensembl lists: eQtlBma lists: EpiGRAPH lists: EpiDISH R package lists: Examl lists: epitopepredict lists: DrivAER lists: Variant Effect Predictor lists: Epigenomics Workflow on Galaxy and Jupyter lists: Eukaryote Genes lists: Evex lists: FateID lists: EXOMEPICKS lists: European Variation Archive (EVA) lists: FANTOM DB lists: Genome Annotation Generator lists: FireDB lists: FGENESH lists: FluoRender lists: FLOSS lists: fineSTRUCTURE lists: FastQC lists: FINDbase Worldwide lists: ExpressYourself lists: fgsea lists: FuncAssociate: The Gene Set Functionator lists: NHLBI Exome Sequencing Project (ESP) lists: FlyBase lists: FlexProt: flexible protein alignment lists: GASV lists: Fugu Genome Project lists: Full-Length cDNA Database lists: FragGeneScan lists: FunRich: Functional Enrichment analysis tool lists: FlowSOM lists: GASSST lists: GeMoMa lists: An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application lists: GEDIT lists: VBASE2 lists: Genome Database for Rosaceae lists: GenePattern Notebook lists: G-Mo.R-Se lists: FusionHunter lists: Genome Projector lists: GeneCodis lists: GEN3VA lists: GENERECON lists: GEMB lists: GeCo3 lists: Gene3D lists: Genomic Annotation in Livestock for positional candidate LOci lists: Gene Expression Atlas lists: GeneProf lists: Genome Trax lists: Genome Reviews lists: GATK lists: FunCluster lists: GFINDer: Genome Function INtegrated Discoverer lists: GermOnline lists: GeneSeeker lists: Gmove lists: Genometa lists: GensearchNGS lists: HARSH lists: Gibbs Motif Sampler lists: Generic GO Term Mapper lists: Genomedata lists: GMcloser lists: GEO2R lists: Gramene lists: Genome Aggregation Database lists: GoMapMan lists: GEPAT lists: Git lists: GNUMAP lists: Generic GO Term Finder lists: Graph2GO lists: Gene Ontology lists: Gaggle lists: GO2MSIG lists: GRASS lists: Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology lists: Genovar lists: HASTE-project lists: H-InvDB lists: Homologous Sequences in Ensembl Animal Genomes lists: Google lists: IMGT/HLA lists: Human Gene Mutation Database lists: GTDB-Tk lists: G protein receptor interaction feature finding instrument lists: HubMed lists: HPEPDOCK Server lists: HUGE - Human Unidentified Gene-Encoded large proteins lists: HAPLOCLUSTERS lists: HiCUP lists: International HapMap Project lists: HiPipe lists: HTR lists: HINT lists: Hybrid-denovo lists: HS-TDT lists: Human Gene Connectome Server lists: HSSP lists: iDASH lists: hyfi: software suite for binding site search lists: HUDSEN lists: IMGT/StatClonotype lists: I-TASSER lists: ImJoy lists: IMEx - The International Molecular Exchange Consortium lists: IMG System lists: HCLUST lists: Human Splicing Finder lists: lme4 lists: Identifiers.org lists: IPD - Immuno Polymorphism Database lists: IntEnz- Integrated relational Enzyme database lists: IBIS: Inferred Biomolecular Interactions Server lists: IMGT - the international ImMunoGeneTics information system lists: Integr8 : Access to complete genomes and proteomes lists: IMGT HighV-QUEST lists: Isaac lists: Interolog/Regulog Database lists: InterProScan lists: IRESite lists: IPI lists: inGAP lists: ISFinder lists: KGGSeq lists: iPiG lists: IsoLasso lists: J-Express lists: JGI Genome Portal lists: IsaCGH lists: lncRNAdb lists: LDSELECT lists: IsoEM lists: Database oDatabase of Predicted Subcellular Localization for Eukaryotic PDB Chainsf Predicted Subcellular Localization for Eukaryotic PDB Chains lists: IMG lists: LTR_FINDER_parallel lists: LAST lists: MBGD - Microbial Genome Database lists: jmzML lists: OntoQuest lists: LOCUSMAP lists: MaizeGDB lists: long-read-tools lists: LRPath lists: Magic lists: LS-SNP/PDB lists: LOCATE: subcellular localization database lists: Mammalian Gene Collection lists: Machado lists: MACiE lists: Maqview lists: LitMiner lists: MAKER lists: MEBS: Multigenomic Entropy-Based Score lists: MapSplice lists: Mascot lists: mapDamage lists: MEGAHIT lists: Metabolomics Workbench lists: Libra lists: ML Repo lists: MARRVEL lists: Maq lists: MentaLiST lists: MB-GAN lists: MetaCyc lists: MAP lists: MeQA lists: Metastats lists: MatrixDB lists: MetAMOS lists: MeRIP-PF lists: MendelIHT.jl lists: metaXplor lists: lsa_slurm lists: MetaCyto lists: UEA sRNA Workbench lists: MetaVelvet lists: MMAPPR lists: MBCluster.Seq lists: MIP Scaffolder lists: MERMAID lists: MobiDB lists: MPDA lists: MaSuRCA lists: MICSA lists: MIRIAM Resources lists: miROrtho: the catalogue of animal microRNA genes lists: NCBI lists: proMODMatcher lists: miRBase lists: MethylExtract lists: SCIPION lists: MPscan lists: mirTools lists: MISA lists: MP3 tool lists: Mspire-Simulator lists: Multi-omics Visualization Platform lists: mrCaNaVaR lists: MoDIL lists: MultiLoc lists: MULTIDISEQ lists: Noncoding RNA database lists: MRFSEQ lists: MizBee lists: Multiple Myeloma survival predictor lists: Mouse Phenome Database (MPD) lists: Nucleic Acid Database lists: Myriads lists: miRpathDB lists: MUMmer lists: mzMatch lists: NeLS lists: NEST Simulator lists: MutPred lists: NEMBASE lists: Open Babel lists: NetMHCpan Server lists: MULTIMAP lists: NCBI Genome Workbench lists: Nephele lists: NCBI Probe lists: Ngmlr lists: Necklace lists: NetNGlyc lists: NucleoFinder lists: NeuroMatic lists: Genotyping lists: NGSView lists: NOrMAL lists: Opera lists: NURD lists: ngLOC lists: NeSSM lists: NanoGalaxy lists: ObjTables lists: nmrML lists: nsSNPAnalyzer lists: OsiriX Medical Imaging Software lists: parSMURF lists: Open Trials lists: Ngs backbone lists: PartiGeneDB lists: Pfam lists: Oncodrive-fm lists: Online Resource for Community Annotation of Eukaryotes lists: PanoramaWeb lists: Omics Data Paper Generator lists: Pathway Tools lists: PDBe - Protein Data Bank in Europe lists: Pash 3.0 lists: Orientations of Proteins in Membranes database lists: Pathbase lists: PEDHUNTER lists: PAZAR lists: Peakzilla lists: PeakAnalyzer lists: Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers lists: Pedigree-Draw lists: OLego lists: Parliament2 lists: PEDIGREEQUERY lists: PeakSeq lists: PEDPEEL lists: PhaseME lists: PHI-base lists: PHYLIP lists: PDB Finder lists: Phylogeny.fr lists: PRICE lists: PennSeq lists: Illuminating the Druggable Genome lists: Philius lists: Phenotypes and eXposures Toolkit lists: PhyloPat lists: PicTar lists: Eddy Lab Software lists: Protein Information Resource lists: PhyML lists: PhenoMan lists: PeptideAtlas lists: PIRSF lists: Polygenic Pathways lists: PLANTTFDB lists: pNovo+ lists: PLINK/SEQ lists: PEMA lists: pFind Studio: pLink lists: PM4NGS lists: PrimerBank lists: ProSight Lite lists: PolymiRTS lists: Phospho.ELM lists: Plant Co-expression Annotation Resource lists: Rampart lists: Protein Prospector lists: ProteomeXchange lists: PRED-TMBB lists: Proteomics Identifications (PRIDE) lists: PS-Plant Framework lists: ProtChemSI lists: PRADA lists: Pyntacle lists: PubCrawler lists: ProfCom - Profiling of complex functionality lists: PrimerSeq lists: PyBEL lists: PubChem lists: PubGene lists: R/QTLBIM lists: QGene lists: QMSIM lists: QmRLFS-finder lists: PolyPhred lists: QSRA lists: Preseq lists: ReactomePA lists: QuickGO lists: QUMA lists: RAREMETAL lists: REDItools lists: The Human Protein Atlas lists: rSNP Guide lists: PyRosetta lists: RefSeq lists: RaptorX lists: Reaper - Demultiplexing trimming and filtering sequencing data lists: RegulonDB lists: RESID lists: R Project for Statistical Computing lists: Reactome lists: Rdisop lists: RepeatModeler lists: RESCUE-ESE lists: Relate lists: Reptile lists: R-SAP lists: riborex lists: RNA-SeQC lists: QuPath lists: RNA FRABASE - RNA FRAgments search engine and dataBASE lists: RADAR-base lists: RiboTaper lists: SAMMate lists: rna-stability lists: RightField lists: SASGENE lists: RNAplex lists: runBioSimulations lists: ResponseNet lists: SilkDB lists: Scansite lists: Research-tested Intervention Programs (RTIPs) lists: sapFinder lists: SeqtrimNEXT lists: RNA Virus Database lists: SALT lists: SEEK lists: Seqtk lists: REDfly Regulatory Element Database for Drosophilia lists: SAFA Footprinting Software lists: SeqExpress lists: ROMPREV lists: SeqSaw lists: SeqEM lists: SHELX lists: rSeq lists: SHARCGS lists: rnaSPAdes lists: SimSeq lists: SGA lists: Sherman lists: SeQuiLa lists: SGD lists: ShinyGO lists: SISYPHUS lists: SVA lists: ASC lists: SIMULATE lists: SILVA lists: SNP HITLINK lists: SIBLINK lists: SKAT lists: SimRare lists: SnoopCGH lists: SMRT View lists: SASQUANT lists: SIMPED lists: Sniffles lists: SIBMED lists: SMI Services lists: SOAPnuke lists: SGN lists: SIDER lists: SMART lists: ShortFuse lists: SWEEP lists: SnpSift lists: SOAPfusion lists: SNPTEST lists: SwissTree lists: TopFIND lists: Solas lists: SoupX lists: STEPS lists: FASTSLINK lists: SpliceMap lists: StSNP lists: Supersplat lists: Sybil lists: TAPIR: target prediction for plant microRNAs lists: SWISS-2DPAGE lists: SISSRs lists: T-lex lists: SUMSTAT lists: TAGS lists: Spot lists: TDR Targets Database lists: TDT-PC lists: SpoTyping lists: SynTView lists: SynergyFinder lists: TRAL lists: SPIKE lists: Transporter Classification Database lists: TransmiR lists: TASSEL lists: SYFPEITHI: A Database for MHC Ligands and Peptide Motifs lists: FLUX CAPACITOR lists: TB PORTALS lists: TAndem Splice Site DataBase lists: VirusHunter lists: topGO lists: TMAJ lists: ApiDB ToxoDB lists: tradeSeq lists: TreeDyn lists: Trans-ABySS lists: IQ-TREE lists: Biological General Repository for Interaction Datasets (BioGRID) lists: Trowel lists: TomoMiner lists: UTRdb/UTRsite lists: TWOLOC lists: V-Phaser 2 lists: TropGENE DB lists: Trim Galore lists: TRACESPipe lists: Gene Index Project lists: Tool recommender system in Galaxy lists: WEIGHTED FDR lists: UTGB Toolkit lists: xia2 pipeline lists: USeq lists: TRiCoLOR lists: UniParc lists: VAAST lists: variancePartition lists: VirusSeq lists: Webproanalyst lists: XPN lists: WSsas - Web Service for the SAS tool lists: UNAFold lists: zUMIs lists: VaDiR lists: Yeast Search for Transcriptional Regulators And Consensus Tracking lists: Vector Alignment Search Tool lists: Zebrafish Information Network (ZFIN) lists: YASARA lists: Vmatch lists: VFDB - Virulence Factors of Bacterial Pathogens lists: Xenbase lists: Visualization and Analysis of Networks containing Experimental Data (VANTED) lists: VisSR lists: AutoDock lists: dbEST lists: DESeq2 lists: DNA DataBank of Japan (DDBJ) lists: FASTX-Toolkit lists: SUP lists: Trimmomatic lists: VIPERdb lists: ABySS lists: AdapterRemoval lists: Alien-hunter lists: ALTree lists: Integrative Genomics Viewer lists: RDKit: Open-Source Cheminformatics Software lists: Acacia lists: AMAP lists: Anfo lists: Aragorn lists: Arden lists: Ariba lists: ART lists: Augustus lists: Axe lists: Baitfisher lists: BALLView lists: BEAGLE lists: BEDOPS lists: eXpress lists: BOXSHADE 3.21 lists: Cassiopee lists: Cdbfasta lists: Circlator lists: Clearcut lists: Clonalframe lists: ClonalOrigin lists: Computational Morphometry Toolkit lists: Concavity lists: CRAC lists: cwltool lists: Daligner lists: Datamash lists: DNACLUST lists: DWGSIM lists: Eigensoft lists: EMBOSS lists: ESTScan lists: EULER-SR lists: FASTLINK lists: FigTree lists: fitGCP lists: Fsm-lite lists: Gamgi lists: GASiC lists: Ghemical lists: GIIRA lists: Grinder lists: Gwyddion lists: Hmmer lists: HTQC lists: IDBA-UD lists: ImageJ lists: Infernal lists: PyMOL lists: GenABEL lists: Biopython lists: QuorUM lists: Prodigal lists: QuteMol lists: PRESTO: Genetic Association Analysis Software lists: Probalign lists: Computational Structural Biology Toolbox lists: LEfSe lists: Happy lists: jModelTest lists: KMC lists: LAMARC lists: libRoadRunner lists: LoFreq lists: MetaPhlAn lists: MicrobiomeUtilities lists: MINIMAC lists: MIPE lists: mothur lists: Mugsy lists: GNU Octave lists: Oncofuse lists: PBSIM lists: PerlPrimer lists: PHAST lists: Picard lists: PLINK lists: ADEGENET lists: phytools lists: PSCBS lists: R/QTL lists: SAM lists: vegan lists: RepeatMasker lists: Scythe lists: SEER lists: Seq-Gen lists: SMRT-Analysis lists: Scalable Nucleotide Alignment Program lists: SPAdes lists: TraceTuner lists: Transterm lists: TreeView lists: Viewmol lists: Vascular Modeling Toolkit lists: Aegean lists: amide lists: Anndata lists: ANTS - Advanced Normalization ToolS lists: ARB project lists: ArtificialFastqGenerator lists: Arvados lists: Bandage lists: Berkeley Advanced Reconstruction Toolbox lists: BBmap lists: Eagle lists: Bio-Formats lists: BioImage Suite lists: BioJava Project lists: BioSig: An Imaging Bioinformatics System for Phenotypic Analysis lists: BRAKER lists: Bustools lists: Computerized Anatomical Reconstruction and Editing Toolkit lists: CellProfiler Image Analysis Software lists: ChIPSeq Peak Finder lists: ChromHMM lists: Cluster lists: Cytoscape lists: Dazzler lists: DCMTK: DICOM Toolkit lists: DeepNano lists: dinifti lists: DICOMscope lists: Dipy lists: Drop-seq tools lists: Electronic Cell Project lists: Ecopcr lists: Edtsurf lists: DOMAINATRIX lists: DOMALIGN lists: Embassy-domsearch lists: E-mem lists: e-PCR lists: Falcon lists: Fastaq lists: Fastqtl lists: Ffindex lists: FreeSurfer lists: FSA lists: FSL lists: Galaxy lists: GARLI lists: Garlic lists: IndelGenotyper lists: gdpc lists: Gemma lists: GenomeTools lists: Gentle lists: GERP lists: Gff2aplot lists: gffread lists: GraPhlAn lists: Gubbins lists: Harvest-tools lists: HiLive lists: Hinge lists: ImageMagick lists: ImageVis3D lists: Indelible lists: InVesalius 3 lists: IQ TREE lists: ITK-SNAP lists: JBrowse lists: JIST: Java Image Science Toolkit lists: Fastahack lists: Lipsia lists: LUMPY lists: Mash lists: Mesquite lists: MetaBAT lists: MOSAIK lists: MRtrix lists: Human Disease Ontology lists: NanoFilt lists: Object-Oriented Development Interface for NMR lists: OpenElectrophy lists: OpenMEEG lists: OpenWalnut lists: OptiType lists: PARASAIL lists: ParaView lists: PhyloPhlAn lists: Phyutility lists: Porechop lists: PSIPRED lists: PsychoPy lists: Pychopper lists: pydicom lists: PySurfer lists: MNE software lists: pbcore lists: pyxnat lists: QIIME2 lists: RAxML Next Generation lists: ShortRead lists: Phangorn lists: psych lists: VennDiagram lists: Recognition of Errors in Assemblies using Paired Reads lists: RELION lists: RStudio lists: Salmon lists: Scoary lists: University of Zurich SCRM - Cell-and Tissue Biobank lists: Short Read Sequence Typing for Bacterial Pathogens lists: Umap lists: VoxBo lists: WTDBG lists: XNAT - The Extensible Neuroimaging Archive Toolkit lists: ABACAS lists: AceDB lists: LINKAGE lists: Protein Information Resource lists: PredictNLS lists: tRNAscan-SE lists: RSEM lists: Aeskulap lists: alleleCount lists: assembly-stats lists: Atropos lists: Assemblytics lists: Augur lists: AxParafit lists: Aghermann lists: bambamc lists: AxPcoords lists: bamkit lists: BAli-Phy lists: Auspice lists: BBHash lists: BCALM 2 lists: Bibus lists: BioMAJ lists: BioCocoa lists: Biber lists: BioImageXD lists: caftools lists: BOLT-LMM lists: CamiTK lists: CLI for BioMAJ lists: CAMP lists: CAT and BAT lists: CHIME lists: CDK lists: ChromImpute lists: CiftiLib lists: conda-package-handling lists: CARD lists: CONTRAfold lists: CodonW lists: Change-O lists: C Thread Pool lists: Chemtool lists: covtobed lists: CTK lists: CTDopts lists: CTDConverter lists: Conquest DICOM lists: CTSim lists: Dicom3tools lists: Dendroscope3 lists: cyvcf2 lists: Deepbinner lists: EDFlib lists: EDFbrowser lists: dicompyler lists: EMMAX lists: DEXTRACTOR lists: DNApi lists: Epigrass lists: ELPH lists: ExaBayes lists: EMPeror lists: FreeImage lists: Fast5 Library lists: Entangle lists: FFP lists: GenomeTester4 lists: Filtlong lists: EMBOSS explorer lists: GfaPy lists: GATB lists: GCLib lists: EpiFire lists: HTSJDK lists: GDCM lists: GNUmed lists: GraphMap2 lists: foreign lists: Ginkgo CADx lists: GramAlign lists: IDeFIX lists: ImageTooth lists: Htscodecs lists: IGoR lists: iVar lists: InsPecT lists: Intake lists: IgDiscover lists: JAligner lists: ISMRMRD lists: JabRef lists: Lambda lists: Kaptive lists: KBibTeX lists: InSilicoSeq lists: kineticsTools lists: AcePerl lists: KmerResistance lists: Bio-EUtilities lists: Insight Toolkit lists: Kleborate lists: KMA lists: kempbasu lists: Bio-ASN1-EntrezGene lists: IVA lists: Bio-Coordinate lists: Bio-Graphics lists: AI-FANN lists: Bio-Chado-Schema lists: BioD lists: Bio-Tools-Run-Alignment-Clustalw lists: Bio-PrimerDesigner lists: Bioparser lists: Edlib lists: Bio-SamTools lists: libdisorder lists: libncl lists: Bio-Tools-Run-Alignment-TCoffee lists: Chado lists: Bio-Tools-Phylo-PAML lists: libGDF lists: JLODA lists: libdivsufsort lists: libminc lists: Bio-SCF lists: Sort-Key-Top lists: Java NeXML libraries and tools lists: libmaus2 lists: libqes lists: MIA lists: libics lists: FAST Analysis of Sequences Toolbox lists: Libchipcard lists: TaxonomyTree lists: Core Wrapper lists: Lighter lists: SSW Library lists: libqc++ lists: SeqLib lists: tabixpp lists: libStatGen lists: ThreadPool lists: Lucy lists: MafFilter lists: Metastudent lists: Libxdf lists: limereg lists: Mapsembler2 lists: MAXFLOW lists: metaBIT lists: MacSyFinder lists: VIGRA lists: MCL lists: MHAP lists: MindTheGap lists: Logol lists: medicalterms lists: mmtf-python lists: Miniasm lists: Tab2MAGE lists: MView lists: LTRsift lists: Molekel lists: mirtop lists: Maude lists: MicrobeGPS lists: mPSQed lists: mPTP lists: SMILE lists: Entrez Direct lists: NW-align lists: NanoSV lists: Mustang lists: Nanocall lists: Ngila lists: MRtrix3 lists: NORSp lists: Murasaki lists: Nextflow lists: NCBI accession download script lists: omegaMap lists: NJplot lists: NanoLyse lists: OpenCFU lists: NORSnet lists: OBITools lists: NeoBio lists: OptimiR lists: PartitionFinder lists: OpenSurgSim lists: NanoPlot lists: NextSV lists: OpenEMR lists: Orthanc lists: PAIPline lists: Odil lists: PHYLOViZ lists: PlasmidSeeker lists: PDB2PQR lists: OpenIGTLink lists: Parsnp lists: parallel-fastq-dump lists: ParsInsert lists: PiGx-RNAseq lists: PfTools lists: PlasmidID lists: Phyx lists: pipasic lists: pngquant lists: pbcopper lists: Patristic lists: PLIP lists: Placnet lists: PhySamp lists: pufferfish lists: PRINSEQ lists: PLAST lists: PCMA lists: picopore lists: POA lists: PROFisis lists: ProDA lists: PRANK lists: Cooler lists: pyepl lists: pssh2 lists: Plastimatch lists: pynast lists: psignifit lists: python-airr lists: Populations lists: pyFAI lists: python-biom-format lists: pyranges lists: purple lists: PyCogent lists: qtlreaper lists: qcumber lists: python-bx lists: pyomo lists: pycoqc lists: Proteinortho lists: DendroPy lists: qtltools lists: pyscanfcs lists: rambo-k lists: qcat lists: rasmol lists: rampler lists: raccoon lists: ragout lists: rapmap lists: quicktree lists: Raster3D lists: AnnotationHub lists: Rate4Site lists: altcdfenvs lists: annotate lists: biomformat lists: Biobase lists: affyio lists: bridgedbr lists: BiocGenerics lists: biovizBase lists: genefilter lists: CNEr lists: bsgenome lists: geneplotter lists: ctc lists: genomicalignments lists: go.db lists: genomeinfodb lists: hypergraph lists: gviz lists: groHMM lists: mergeomics lists: impute lists: makecdfenv lists: multiassayexperiment lists: qusage lists: mutationalpatterns lists: metagenomeseq lists: preprocesscore lists: pwmenrich lists: rbgl lists: htsfilter lists: nanostringqcpro lists: rgsepd lists: rcpi lists: pcaMethods lists: adephylo lists: rsamtools lists: savr lists: tfbstools lists: xvector lists: ade4 lists: biwt lists: beeswarm lists: cmprsk lists: alakazam lists: bio3d lists: Epi lists: BoolNet lists: DT lists: DoseFinding lists: itertools lists: fitdistrplus lists: fitbitscraper lists: dynamicTreeCut lists: epibasix lists: distory lists: forecast lists: incidence lists: hms lists: nmf lists: mediana lists: genetics lists: lexrankr lists: psychometric lists: optimalcutpoints lists: proc lists: pcapp lists: parmigene lists: rann lists: phylobase lists: psyphy lists: psychotree lists: rnexml lists: rook lists: rpact lists: tigger lists: robustrankaggreg lists: qqman lists: rwave lists: shazam lists: rsvd lists: rncl lists: rotl lists: rniftilib lists: sjplot lists: wavethresh lists: stringi lists: snowfall lists: waveslim lists: surveillance lists: tsne lists: webgestaltr lists: resfinder lists: readucks lists: recan lists: roadtrips lists: readseq lists: roguenarok lists: rtax lists: rgfa lists: ruby-bio lists: runcircos-gui lists: sailfish lists: samclip lists: saint lists: sambamba lists: seqmagick lists: sbmltoolbox lists: seq-seq-pan lists: seqsero lists: seqwish lists: shapeit4 lists: sepp lists: crb-blast lists: sigma-align lists: sibsim4 lists: signalalign lists: sibelia lists: shiny-server lists: sistr lists: skesa lists: sigviewer lists: snpomatic lists: spaced lists: sitplus lists: sofa-apps lists: sra-toolkit lists: strap-base lists: sparta lists: swarm lists: sourmash lists: surankco lists: streamlit lists: tab2mage lists: sumaclust lists: sweed lists: tacg lists: zAlign lists: tiddit lists: Workrave lists: sprai lists: VolPack lists: XMedCon lists: Yanosim lists: Yanagiba lists: libswiss-perl lists: yaha lists: VisIt lists: VelvetOptimiser lists: variation graph lists: vcfanno lists: VarMatch lists: VirulenceFinder lists: CCS lists: VADR lists: VARNA lists: VMD lists: FISH lists: trace2dbEST lists: TREE-PUZZLE lists: umis lists: Trinculo lists: toil lists: TRANSIT lists: toppred lists: Unicycler lists: TM-align lists: Tn-seq explorer lists: Tombo lists: TopHat-Recondition is related to: FreeContact is parent organization of: neurodebian |
Free, Freely available | nlx_151598 | SCR_006638 | SciCrunch Registry | Debian - The universal operating system, Debian GNU/Linux | 2026-10-31 12:14:26 | 52 | |||||||
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IntAct Resource Report Resource Website 1000+ mentions |
IntAct (RRID:SCR_006944) | IntAct | data or information resource, data repository, database, service resource, storage service resource | Open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions. Direct user submissions of molecular interaction data are encouraged, which may be deposited prior to publication in a peer-reviewed journal. The IntAct Database contains (Jun. 2014): * 447368 Interactions * 33021 experiments * 12698 publications * 82745 Interactors IntAct provides a two-tiered view of the interaction data. The search interface allows the user to iteratively develop complex queries, exploiting the detailed annotation with hierarchical controlled vocabularies. Results are provided at any stage in a simplified, tabular view. Specialized views then allows "zooming in" on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available. | protein domain, motif, protein interaction, molecular interaction, interaction, protein, binary interaction, complex, data set, protein-protein interaction, pathway, small molecule-protein, nucleic acid-protein, small molecule, nucleic acid, protein binding, chromatin, cancer, apoptosis, molecular biology, virus, source code, isoform, gold standard |
is used by: ChannelPedia is used by: MINT is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: 3DVC is listed by: re3data.org is listed by: OMICtools is related to: 3D-Interologs is related to: IMEx - The International Molecular Exchange Consortium is related to: MPIDB is related to: TissueNet - The Database of Human Tissue Protein-Protein Interactions is related to: InteroPorc is related to: Interaction Reference Index is related to: Pathway Commons is related to: ConsensusPathDB is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: Integrated Molecular Interaction Database is related to: VirHostNet: Virus-Host Network is related to: PSICQUIC Registry is related to: UniProt is related to: SIB Swiss Institute of Bioinformatics is related to: I2D is related to: InnateDB is related to: MatrixDB is related to: MBInfo is related to: AgBase is related to: Cardiovascular Gene Ontology Annotation Initiative is related to: PSI-MI is related to: Agile Protein Interactomes DataServer has parent organization: European Bioinformatics Institute works with: IMEx - The International Molecular Exchange Consortium |
European Union contract FP7-HEALTH-2007-223411; European Union contract FP7-HEALTH-2007-200767 |
PMID:24234451 PMID:22121220 PMID:19850723 PMID:17145710 PMID:14681455 |
Apache License, v2, (software), Creative Commons Attribution License, (data), The community can contribute to this resource | OMICS_01918, r3d100010671, nif-0000-03026 | https://doi.org/10.17616/R3QS4R | SCR_006944 | SciCrunch Registry | IntAct | 2026-10-31 12:14:41 | 1955 | ||||
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InterPro Resource Report Resource Website 5000+ mentions |
InterPro (RRID:SCR_006695) | InterPro | analysis service resource, data access protocol, data analysis service, data or information resource, database, production service resource, service resource, software resource, web service | Service providing functional analysis of proteins by classifying them into families and predicting domains and important sites. They combine protein signatures from a number of member databases into a single searchable resource, capitalizing on their individual strengths to produce a powerful integrated database and diagnostic tool. This integrated database of predictive protein signatures is used for the classification and automatic annotation of proteins and genomes. InterPro classifies sequences at superfamily, family and subfamily levels, predicting the occurrence of functional domains, repeats and important sites. InterPro adds in-depth annotation, including GO terms, to the protein signatures. You can access the data programmatically, via Web Services. The member databases use a number of approaches: # ProDom: provider of sequence-clusters built from UniProtKB using PSI-BLAST. # PROSITE patterns: provider of simple regular expressions. # PROSITE and HAMAP profiles: provide sequence matrices. # PRINTS provider of fingerprints, which are groups of aligned, un-weighted Position Specific Sequence Matrices (PSSMs). # PANTHER, PIRSF, Pfam, SMART, TIGRFAMs, Gene3D and SUPERFAMILY: are providers of hidden Markov models (HMMs). Your contributions are welcome. You are encouraged to use the ''''Add your annotation'''' button on InterPro entry pages to suggest updated or improved annotation for individual InterPro entries. | protein, classify, prediction, protein domain, genome, protein family, functional site, protein sequence, protein function, analysis, nucleic acid, amino acid, amino acid sequence, gold standard |
is listed by: re3data.org is listed by: OMICtools is related to: TIGRFAMS is related to: TIGRFAMS is related to: FlyMine is related to: GeneSpeed- A Database of Unigene Domain Organization is related to: Biomine is related to: InterProScan is related to: GeneTerm Linker is related to: Gene Ontology is related to: ProDom is related to: Algal Functional Annotation Tool has parent organization: European Bioinformatics Institute |
European Union FP7 Scientific Data Repositories 213037; BBSRC BB/F010508/1; NIGMS GM081084 |
PMID:22096229 PMID:21082426 PMID:18940856 PMID:18428686 PMID:18025686 PMID:17202162 PMID:16909843 PMID:15608177 PMID:12520011 PMID:12230031 PMID:11159333 PMID:11119311 PMID:11125043 |
Acknowledgement requested, Free, Public, The community can contribute to this resource | nif-0000-03035, OMICS_01694, r3d100010798 | https://doi.org/10.17616/R3FS61 | SCR_006695 | SciCrunch Registry | InterPro: protein sequence analysis & classification, InterPro protein sequence analysis and classification | 2026-10-31 12:14:34 | 7722 | ||||
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European Bioinformatics Institute Resource Report Resource Website 1000+ mentions |
European Bioinformatics Institute (RRID:SCR_004727) | EMBL-EBI | institution | Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL. | organization, academic, bioinformatics, research, service, data, computational, biology, training, database, DNA, protein |
is used by: Blueprint Epigenome is listed by: re3data.org is related to: AgedBrainSYSBIO is related to: ProteomeXchange is related to: Open PHACTS is related to: RHEA is related to: TraCeR is related to: 3D-Beacons is related to: RNAcentral has parent organization: European Molecular Biology Laboratory is parent organization of: CoGenT++ is parent organization of: ENA Sequence Version Archive is parent organization of: Reaper - Demultiplexing trimming and filtering sequencing data is parent organization of: PeakAnalyzer is parent organization of: Tally is parent organization of: Clustal Omega is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology is parent organization of: The Alternatve Splicing Database is parent organization of: BioModels is parent organization of: CHEBI is parent organization of: MAGE is parent organization of: Ensembl is parent organization of: MIAME is parent organization of: UniProt is parent organization of: Ligand-Gated Ion Channel Database is parent organization of: EBI Genomes is parent organization of: IMEx - The International Molecular Exchange Consortium is parent organization of: Toolbox at the European Bioinformatics Institute is parent organization of: Clustal W2 is parent organization of: ArrayExpress is parent organization of: IMGT/HLA is parent organization of: IntEnz- Integrated relational Enzyme database is parent organization of: IPD - Immuno Polymorphism Database is parent organization of: IPI is parent organization of: MicroArray and Gene Expression Markup Language is parent organization of: DaliLite Pairwise comparison of protein structures is parent organization of: Chemical Information Ontology is parent organization of: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees is parent organization of: Proteomics Identifications (PRIDE) is parent organization of: Software Ontology is parent organization of: FSSP - Families of Structurally Similar Proteins is parent organization of: Experimental Factor Ontology is parent organization of: Identifiers.org is parent organization of: HipSci is parent organization of: ProteomeXchange is parent organization of: Taxonomy is parent organization of: PDBe - Protein Data Bank in Europe is parent organization of: EBI Dbfetch is parent organization of: ProFunc is parent organization of: WSDbfetch (SOAP) is parent organization of: QuickGO is parent organization of: SAS - Sequence Annotated by Structure is parent organization of: UniProt DAS is parent organization of: UniParc at the EBI is parent organization of: Patent Abstracts is parent organization of: BioSample Database at EBI is parent organization of: Database of Genomic Variants Archive (DGVa) is parent organization of: European Genome phenome Archive is parent organization of: UniSave is parent organization of: ArchSchema is parent organization of: UniRef at the EBI is parent organization of: EBIMed is parent organization of: Kraken is parent organization of: SIMBioMS is parent organization of: Expression Profiler is parent organization of: Whatizit is parent organization of: InterProScan is parent organization of: VectorBase is parent organization of: DRCAT Resource Catalogue is parent organization of: FunTree is parent organization of: CREATE is parent organization of: BioMedBridges is parent organization of: PSICQUIC Registry is parent organization of: PDBsum is parent organization of: European Nucleotide Archive (ENA) is parent organization of: DrugPort is parent organization of: Ontology Lookup Service is parent organization of: EDAM Ontology is parent organization of: InterPro is parent organization of: MIRIAM Resources is parent organization of: EB-eye Search is parent organization of: SBO is parent organization of: Ensembl Genomes is parent organization of: NeuronVisio is parent organization of: IntAct is parent organization of: WSsas - Web Service for the SAS tool is parent organization of: Enzyme Structures Database is parent organization of: EMBOSS CpGPlot/CpGReport/Isochore is parent organization of: PaperMaker is parent organization of: CluSTr is parent organization of: Genome Reviews is parent organization of: GOA is parent organization of: Integr8 : Access to complete genomes and proteomes is parent organization of: IPD-ESTDAB- The European Searchable Tumour Line Database is parent organization of: IPD-HPA - Human Platelet Antigens is parent organization of: IPD-KIR - Killer-cell Immunoglobulin-like Receptors is parent organization of: IPD-MHC- Major Histocompatibility Complex is parent organization of: HilbertVis is parent organization of: Gene Expression Atlas is parent organization of: Parasite genome databases and genome research resources is parent organization of: Alternative Exon Database is parent organization of: AltExtron Database is parent organization of: Patent Data Resources is parent organization of: Pompep is parent organization of: Mouse finder is parent organization of: Gene Regulation Ontology is parent organization of: CiteXplore literature searching is parent organization of: MaxSprout is parent organization of: SRS is parent organization of: MicroCosm Targets is parent organization of: Kalign is parent organization of: MUSCLE is parent organization of: FASTA is parent organization of: WU-BLAST is parent organization of: Oases is parent organization of: HTS Mappers is parent organization of: CRAM is parent organization of: CSA - Catalytic Site Atlas is parent organization of: ArrayExpress (R) is parent organization of: WiggleTools is parent organization of: vsn is parent organization of: rlsim is parent organization of: ISA Infrastructure for Managing Experimental Metadata is parent organization of: BioMart Project is parent organization of: BioPerl is parent organization of: BioJS is parent organization of: EMDataResource.org is parent organization of: HTqPCR is parent organization of: Reactome is parent organization of: Europe PubMed Central is parent organization of: h5vc is parent organization of: LexGrid is parent organization of: Consensus CDS is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: OrChem is parent organization of: Orphanet Rare Disease Ontology is parent organization of: Reflect is parent organization of: BioLayout Express 3D is parent organization of: Virtual Fly Brain is parent organization of: GeneWise is parent organization of: PhenoMeNal is parent organization of: Ensembl Metazoa is parent organization of: Velvet |
BBSRC ; EMBL member states ; European Union ; Industry Programme partners ; NIH ; UK Research Councils ; Wellcome Trust |
grid.225360.0, Wikidata: Q1341845, ISNI: 0000 0000 9709 7726, nlx_72386 | https://ror.org/02catss52 | SCR_004727 | SciCrunch Registry | EBI, European Molecular Biology Laboratory - European Bioinformatics Institute | 2026-10-31 12:13:49 | 3760 | ||||||
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3DVC Resource Report Resource Website |
3DVC (RRID:SCR_001377) | 3DVC | community building portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE, confirmed by curator 11/21/2018; Community of researchers attempting to build a comprehensive virtual cell model. The 3DVC will do for cell biology what the Large Hadron Collider (LHC) does for particle physics, but through a virtual rather than physical resource. It will bring together collaborators around a shared infrastructure to advance the field through efficient groundbreaking science and technology, the results of which will be broadly disseminated to an audience ranging from K12 to professionals. The 3DVC is committed to open science, yet strives for sustainability through new business models that leverages that open content. | cell, model, biological structure, molecule |
lists: Albinism database lists: ButterflyBase lists: G2P Knowledge Centre lists: Bio-Job.org lists: RettBASE: IRSF MECP2 Variation Database lists: Resource for Biocomputing Visualization and Informatics lists: National Center for Integrative Biomedical Informatics lists: Genome Network Platform lists: NeuroExplorer lists: Open Provenance Model lists: BarleyBase lists: BioModels lists: Arabidopsis Reactome lists: MEDLINE lists: bioDBcore lists: GermOnline lists: GlycoMapsDB lists: SNPHunter lists: Allen Institute for Brain Science Sleep Study lists: Coddle-Codons Optimized to Discover Deleterious LEsions lists: MicroArray and Gene Expression Markup Language lists: Fungal Genome Initiative lists: EMDataResource.org lists: University of Southern California LONI Software lists: Ontology Development and Information Extraction lists: Software Distribution Sets lists: L-Measure lists: UCSF Chimera lists: Zebrafish Neurophenome Project Database lists: Standards-based Infrastructure with Distributed Resources lists: HapMap 3 and ENCODE 3 lists: NCBI BioProject lists: SEQanswers Wiki lists: NIF Data Federation lists: SMD lists: SoyBase lists: modelcrop.org lists: BiGG Database lists: FSST - Functional Similarity Search Tool lists: LHP LHDL lists: Open Provenance Model Vocabulary lists: DiseaseMeth lists: neuroVIISAS lists: Predictive Networks lists: SitEx lists: NRCAM lists: DisGeNET lists: MCMBB lists: BARD lists: Mouse Genome Informatics (MGI) lists: European Nucleotide Archive (ENA) lists: Comparative Toxicogenomics Database (CTD) lists: PomBase lists: Stanford University HIV Drug Resistance Database lists: Database of Chemical Compounds and Reactions in Biological Pathways lists: UCSD-Nature Signaling Gateway Molecule Pages lists: IntAct lists: The WWW Virtual Library: Model Organisms lists: Helicobacter Pylori Database of Protein Interactomes lists: Genes to Cognition: Neuroscience Research Programme lists: neuroConstruct lists: ModelDB lists: 3DViewnix lists: TMRPres2D lists: Ikaros Project lists: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING lists: Interagency Modeling and Analysis Group lists: Annozilla (Annotea on Mozilla) lists: Artificial Selected Proteins/Peptides Database lists: Cancer Chromosomes lists: CATMA - Complete Arabidopsis Transcriptome MicroArray lists: Combinatorial Extension (CE) lists: ChemDB: The UC Irvine ChemDB lists: CluSTr lists: CTDatabase lists: DRC - Database of Ribosomal Crosslinks lists: Gene Expression in Tooth Database lists: GenoBase lists: GPX-Macrophage lists: Hetero-compound Information Centre- Uppsala lists: IMG lists: InSatDb lists: InterDom lists: IPD-HPA - Human Platelet Antigens lists: Max Planck Unified Proteome Database lists: Molecular Modelling DataBase lists: MegaMotifbase lists: Metalloprotein Site Database lists: MitoDat - Mendelian Inheritance and the Mitochondrion lists: Madison Metabolomics Consortium Database lists: Olfactory Receptor DataBase lists: SUPERFAMILY lists: EyeBrowse lists: Allen Institute Mouse Diversity Study lists: BIRD - Bio Info R and D lists: Bioinformatics Links Directory lists: Electroencephalogram Database: Prediction of Epileptic Seizures lists: Human Protein-Protein Interaction Mining Tool lists: Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki lists: Systems Biology Workbench lists: CellML lists: MathML lists: AraCyc lists: Biochemical Pathways database lists: CellML Model Repository lists: Cytokine Family Database lists: Bacterial Genomes lists: U.S. Pig Genome Project lists: ComBase: A Combined Database For Predictive Microbiology lists: GeneWindow lists: Comprehensive Systems-Biology Database lists: Candidate Genes to Inherited Diseases lists: MeGX lists: Mammalian Phosphorylation Resource lists: Efficient Mixed-Model Association lists: Proteome Analyst PA-GOSUB lists: PubCrawler lists: Conical: The Computational Neuroscience Class Library lists: Gene Expression Profile Analysis Suite lists: Adaptive Poisson-Boltzmann Solver lists: Aggrescan: The Hot Spot Finder lists: Distributed Annotation System lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: DNAWorks at Helix Systems lists: Microarray DB lists: Gene Relationships Across Implicated Loci lists: SEQtools lists: DeRisi Lab lists: Protein Subcellular Location Image Database lists: Open Information Integration lists: Metagenomics Program at JGI lists: BrainPeps lists: EGAN: Exploratory Gene Association Networks lists: CBioC lists: OrChem lists: Generic GO Term Finder lists: G-node portal electrophysiology data sharing lists: LegumeIP lists: Roadmap Epigenomics Project lists: TrakEM2 lists: ATID: Alternative Translational Initiation Database lists: linked life data - a semantic data integration platform for the biomedical domain lists: Crux tandem mass spectrometry analysis software lists: CellProfiler Analyst lists: Scirus - for scientific information only lists: SRS lists: KEGG lists: Antibodypedia lists: SWISS-MODEL Repository lists: BTKbase lists: ExTopoDB lists: MINAS - Metal Ions in Nucleic AcidS lists: Tripod lists: NIH electronic Research Materials catalogue lists: Alliance for Cellular Signaling Molecule Pages Database lists: Death Domain database lists: Cube-DB lists: OntoQuest lists: EASE: the Expression Analysis Systematic Explorer lists: Greglist lists: Chloroplast Genome Database lists: Montage RTS2000 lists: BGI-RISe - Beijing Genomics Institute Rice Information System lists: ApiDB CryptoDB lists: Chilibot: Gene and Protein relationships from MEDLINE lists: AutDB lists: DAVID lists: Dataverse Network Project lists: Binding MOAD lists: Biological Magnetic Resonance Data Bank (BMRB) lists: RNAhybrid lists: RegulonDB lists: Artemis: Genome Browser and Annotation Tool lists: Genomedata lists: CATSS - Child and Adolescent Twin Study in Sweden lists: Viking Viewer for Connectomics lists: SpliceDB lists: Galaxy lists: SPM lists: Hyper Cell Line Database lists: MeGX has parent organization: University of California at San Diego; California; USA |
NSF 1216893 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152536 | http://www.3dvcell.org/conference-toward-3d-virtual-cell | SCR_001377 | SciCrunch Registry | 3D Virtual Cell | 2026-10-31 12:12:50 | 0 | |||||
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TrED Resource Report Resource Website 1+ mentions |
TrED (RRID:SCR_005869) | TrED | data analysis software, data or information resource, data processing software, database, software application, software resource | TrED is a database of Trichophyton rubrum, a fungus. The database contains strains, cDNA libraries, pathways, and microarray data as well as a directed set of literature. Trichophyton rubrum is the most common dermatophyte species and the most frequent cause of fungal skin infections in humans worldwide. It''''s a major concern because feet and nail infections caused by this organism is extremely difficult to cure. A large set of expression data including expressed sequence tags (ESTs) and transcriptional profiles of this important fungal pathogen are now available. Careful analysis of these data can give valuable information about potential virulence factors, antigens and novel metabolic pathways. We intend to create an integrated database TrED to facilitate the study of dermatophytes, and enhance the development of effective diagnostic and treatment strategies. All publicly available ESTs and expression profiles of T. rubrum during conidial germination in time-course experiments and challenged with antifungal agents are deposited in the database. In addition, comparative genomics hybridization results of 22 dermatophytic fungi strains from three genera, Trichophyton, Microsporum and Epidermophyton, are also included. ESTs are clustered and assembled to elongate the sequence length and abate redundancy. TrED provides functional analysis based on GenBank, Pfam, and KOG databases, along with KEGG pathway and GO vocabulary. It is integrated with a suite of custom web-based tools that facilitate querying and retrieving various EST properties, visualization and comparison of transcriptional profiles, and sequence-similarity searching by BLAST. TrED is built upon a relational database, with a web interface offering analytic functions, to provide integrated access to various expression data of T. rubrum and comparative results of dermatophytes. It is devoted to be a comprehensive resource and platform to assist functional genomic studies in dermatophytes. | expressed sequence tag, transcriptional profile, fungal pathogen, bmu01672, chuv862.00, mya-3108, cdna, pathway, microarray, classification, blast, unisequence, peptide, annotation |
is related to: Gene Ontology is related to: KEGG is related to: GenBank is related to: Pfam |
Ministry of Science and Technology of China 2006AA020504 | PMID:17650345 | nlx_149408 | SCR_005869 | SciCrunch Registry | TrED - T. rubrum Expression Database, Trichophyton rubrum Expression Database, Trichophyton rubrum Expression Database (TrED) | 2026-10-31 12:14:23 | 5 | ||||||
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Chinese Academy of Sciences; Beijing; China Resource Report Resource Website 50+ mentions |
Chinese Academy of Sciences; Beijing; China (RRID:SCR_012797) | CAS | university | Public university for graduate education, under the direct leadership of the Chinese Academy of Sciences. |
is parent organization of: pFind Studio: pLink is parent organization of: Cascleave is parent organization of: rSNPBase is parent organization of: pNovo+ is parent organization of: pLabel is parent organization of: pBuild is parent organization of: Human Potential Tumor Associated Antigen database is parent organization of: pFind is parent organization of: Linked Neuron Data is parent organization of: QC-Chain is parent organization of: Network Ontology Analysis is parent organization of: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit is parent organization of: Human Protein-Protein Interaction Mining Tool is parent organization of: Database of Domain Interactions and Bindings is parent organization of: Group Information Guided ICA is parent organization of: Groupwise Image Registration Toolbox is parent organization of: Local Label Learning Segmentation is parent organization of: Shanghai Institutes for Biological Sciences; Shanghai; China is parent organization of: GPU-Meta-Storms is parent organization of: EPGD is parent organization of: MethyCancer is parent organization of: inGAP is parent organization of: SysZNF - C2H2 Zinc Finger genes is parent organization of: NONCODE is parent organization of: Systematic Platform for Identifying Mutated Proteins (SysPIMP) is parent organization of: IVDB - Influenza Virus Database is parent organization of: Brainnetome fMRI toolkit is parent organization of: Brainnetome Atlas Viewer is parent organization of: Automatic Tractography-based Parcellation Pipeline |
grid.9227.e, Wikidata: Q530471, ISNI: 119573309, Crossref funder ID: 501100002367, nlx_47801 | https://ror.org/034t30j35 | SCR_012797 | SciCrunch Registry | Chinese Academy of Sciences | 2026-10-31 12:15:44 | 66 | ||||||||
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InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | analysis service resource, data access protocol, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource, web service | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
Biotechnology and Biological Sciences Research Council ; EMBL ; European Union |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html, https://bio.tools/interproscan_4 | SCR_005829 | SciCrunch Registry | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-10-31 12:14:24 | 7512 | |||||
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Scripps Research Institute Resource Report Resource Website 1+ mentions |
Scripps Research Institute (RRID:SCR_001907) | TSRI | institution | Nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California with a sister facility in Jupiter, Florida, the institute has laboratories employing scientists, technicians, graduate students, and administrative and other staff, making it the largest private, non-profit biomedical research organization in the United States and among the largest in the world. | institution, American, medical, research, education, biomedical, private, organization |
uses: DIRECT2experts is related to: Clinical and Translational Science Awards Consortium is related to: The Pancreatic Beta-Cell Consortium is parent organization of: piCALL is parent organization of: GeneChip Operating Software is parent organization of: TSRI-Yates Lab is parent organization of: BioGPS: The Gene Portal Hub is parent organization of: METLIN is parent organization of: AutoDock Vina is parent organization of: ViReMa is parent organization of: Autopack is parent organization of: Integrative Neuroscience Initiative on Alcoholism is parent organization of: Joint Center for Structural Genomics is parent organization of: Functional Glycomics Research is parent organization of: VIPERdb is parent organization of: GOEx - Gene Ontology Explorer is parent organization of: VIPERdb is parent organization of: Zinc Finger Tools is parent organization of: XCMS is parent organization of: Chemoproteomic identification and therapeutic validation of proteins of metabolic significance is parent organization of: Leginon is parent organization of: outbreak.info is parent organization of: Scripps Research Institute Florida Cell Based High Throughput Screening Core Facility is parent organization of: Scripps Research Institute La Jolla Genomics Core Facility |
NIH | grid.214007.0, ISNI: 122199231, Wikidata: Q793867, nif-0000-10475 | https://ror.org/02dxx6824 | SCR_001907 | SciCrunch Registry | The Scripps Research Institute, Scripps Research | 2026-10-31 12:12:58 | 1 |
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