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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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Algal Functional Annotation Tool Resource Report Resource Website |
Algal Functional Annotation Tool (RRID:SCR_012034) | Algal Functional Annotation Tool | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest. | gene, pathway, visualization, annotation, function, protein family, ontology, protein, genomics |
is listed by: OMICtools is related to: Gene Ontology is related to: KEGG is related to: MetaCyc is related to: Reactome is related to: Pfam is related to: InterPro has parent organization: University of California at Los Angeles; California; USA |
DOE ; NAABB ; IGP ; Air Force Office of Scientific Research |
PMID:21749710 | OMICS_02226 | SCR_012034 | SciCrunch Registry | 2026-10-31 12:15:34 | 0 | |||||||
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WebGestalt: WEB-based GEne SeT AnaLysis Toolkit Resource Report Resource Website 1000+ mentions |
WebGestalt: WEB-based GEne SeT AnaLysis Toolkit (RRID:SCR_006786) | WebGestalt | data access protocol, software resource, web application, web service | Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish. | proteomic, gene expression, genome wide association study, statistical analysis, functional genomics, protein protein interaction, pathway, regulatory module, analysis toolkit, web application |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: Entrez Gene is related to: KEGG is related to: Pathway Commons is related to: WikiPathways is related to: PheWAS Catalog is related to: webgestaltr has parent organization: Vanderbilt University; Tennessee; USA |
NCI U24 CA159988; NIAAA U01 AA013512; NIAAA U01 AA016662; NIDA P01 DA015027; NIGMS R01 GM088822; NIMH P50 MH078028; NIMH P50 MH096972 |
PMID:24233776 PMID:15980575 PMID:14975175 |
Free, Freely available | OMICS_02222, nif-0000-30622 | http://bioinfo.vanderbilt.edu/webgestalt/ | SCR_006786 | SciCrunch Registry | GOTM, Gene Ontology Tree Machine, WebGestalt2, WEB-based GEne SeT AnaLysis Toolkit, WebGestalt | 2026-10-31 12:14:35 | 3155 | ||||
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GeneCodis Resource Report Resource Website 100+ mentions |
GeneCodis (RRID:SCR_006943) | GeneCodis | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web-based tool for the ontological analysis of large lists of genes. It can be used to determine biological annotations or combinations of annotations that are significantly associated to a list of genes under study with respect to a reference list. As well as single annotations, this tool allows users to simultaneously evaluate annotations from different sources, for example Biological Process and Cellular Component categories of Gene Ontology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional analysis, gene, annotation, statistical analysis, functional genomics, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: KEGG has parent organization: Spanish National Research Council; Madrid; Spain |
Juan de la Cierva research program ; Spanish Minister of Science and Innovation BIO2010-17527; Government of Madrid P2010/BMD-2305 |
PMID:22573175 PMID:19465387 PMID:17204154 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02221, biotools:genecodis3, nlx_149254 | https://bio.tools/genecodis3 | SCR_006943 | SciCrunch Registry | Gene annotations co-ocurrence discovery, GeneCodis - Gene annotations co-ocurrence discovery | 2026-10-31 12:18:36 | 353 | ||||
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ShinyGO Resource Report Resource Website 1000+ mentions |
ShinyGO (RRID:SCR_019213) | data access protocol, software resource, web service | Software graphical gene set enrichment tool for animals and plants. Graphical web application to gain insights from gene sets. Features include graphical visualization of enrichment results and gene characteristics, and application program interface access to KEGG and STRING for retrieval of pathway diagrams and protein-protein interaction networks. | Graphical gene set enrichment, animal gene, plant gene, graphical visualization, enrichment results, gene characteristics, pathway diagrams retrieval, protein interaction network, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Ensembl is related to: STRING is related to: KEGG has parent organization: South Dakota State University; South Dakota; USA |
PMID:31882993 | biotools:ShinyGO | https://bio.tools/ShinyGO | SCR_019213 | SciCrunch Registry | ShinyGO 0.77, ShinyGO 0.80, Shiny Gene Ontology, ShinyGO v0.61 | 2026-10-31 12:17:14 | 1213 | |||||||
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DAVID Resource Report Resource Website 10000+ mentions |
DAVID (RRID:SCR_001881) | DAVID | data access protocol, data or information resource, database, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis. | functional domain, annotation, motif, protein, ontology enrichment, gene, high-throughput, functional classification, functional annotation, clustering, genome, pathway, gene-disease association, interaction, functional domain, motif, visualization, FASEB list |
is listed by: OMICtools is listed by: 3DVC is listed by: LabWorm is listed by: SoftCite is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG has parent organization: NCI-Frederick |
NCI ; NIAID NO1-CO-56000 |
PMID:19131956 PMID:12734009 PMID:35325185 PMID:22543366 PMID:17980028 PMID:17576678 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30408, OMICS_02220, nif-0000-10451, SCR_003033 | http://david.abcc.ncifcrf.gov/ | SCR_001881 | SciCrunch Registry | DAVID Bioinformatics Resources, Visualization and Integrated Discovery Bioinformatics Resources, Database for Annotation Visualization and Integrated Discovery, The Database for Annotation, The Database for Annotation Visualization and Integrated Discovery Bioinformatics Resources | 2026-10-31 12:12:58 | 20855 | ||||
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Integrated Molecular Interaction Database Resource Report Resource Website 1+ mentions |
Integrated Molecular Interaction Database (RRID:SCR_003546) | IMID | data or information resource, database | Database for molecular interaction information integrated with various other bio-entity information, including pathways, diseases, gene ontology (GO) terms, species and molecular types. The information is obtained from several manually curated databases and automatic extraction from literature. There are protein-protein interaction, gene/protein regulation and protein-small molecule interaction information stored in the database. The interaction information is linked with relevant GO terms, pathway, disease and species names. Interactions are also linked to the PubMed IDs of the corresponding abstracts the interactions were obtained from. Manually curated molecular interaction information was obtained from BioGRID, IntAct, NCBI Gene, and STITCH database. Pathway related information was obtained from KEGG database, Pathway Interaction database and Reactome. Disease information was obtained from PharmGKB and KEGG database. Gene ontology terms and related information was obtained from Gene Ontology database and GOA database. | pathway, disease, gene ontology, specie, interaction, molecular, protein-protein interaction, gene/protein regulation, protein-small molecule interaction, gene, protein, regulation |
is related to: Gene Ontology is related to: Entrez Gene is related to: Pathway Commons is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: IntAct is related to: Search Tool for Interactions of Chemicals is related to: KEGG is related to: Pathway Interaction Database is related to: Reactome is related to: PharmGKB has parent organization: Florida State University; Florida; USA |
PMID:22238258 | nlx_157667 | SCR_003546 | SciCrunch Registry | 2026-10-31 12:20:02 | 1 | ||||||||
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Allen Institute Neurowiki Resource Report Resource Website |
Allen Institute Neurowiki (RRID:SCR_005042) | Allen Neurowiki | controlled vocabulary, data or information resource, database, narrative resource, ontology, wiki | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. The Allen Institute Neurowiki is a joint project between Vulcan Inc. and the Allen Institute to build a Semantic Wiki mapping genetic instances. It is a finished prototype testing the import pipelines and display componenets for combining 5 major RDF datasets from 4 different sources. Current planning includes mapping complete datasets, curating a better ontology, and creating multiple ontology management for a user class. Biological Linked Data Map: * Open, public online access * Data from multiple RDF data stores * Complete import pipeline using LDIF framework * Outlines of each imported instance embedding inline wiki properties and providing views of imported properties from original RDF datasets * Charting tools that ''''pivot'''' SPARQL queries providing several views of each query * Navigation and composition tools for accessing and mining the data Where did we get the data? * KEGG: Kyoto Encyclopedia of Genes and Genomes: KEGG GENES is a collection of gene catalogs for all complete genomes generated from publicly available resources, mostly NCBI RefSeq * Diseasome: The Diseasome website is a disease / disorder relationships explorer and a sample of an innovative map-oriented scientific work. Built by a team of researchers and engineers, it uses the Human Disease Network dataset. * DrugBank: The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information. * Sider: Sider contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. Every piece of content on every instance page is generated by Semantic Result Formatters interpreting SPARQL results. | gene, disease, drug, effect, pathway, sparql, triplestore, probe, structure |
is related to: KEGG is related to: Diseasome is related to: DrugBank is related to: SIDER has parent organization: Allen Institute for Brain Science |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144032 | SCR_005042 | SciCrunch Registry | Biological Linked Data Map, Neurowiki: Biological Linked Data Map, Neurowiki, Allen Neurowiki: Biological Linked Data Map, Allen Institute Neurowiki: Biological Linked Data Map | 2026-10-31 12:14:02 | 0 | |||||||
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SEGS Resource Report Resource Website 1+ mentions |
SEGS (RRID:SCR_003554) | SEGS | analysis service resource, data analysis service, production service resource, service resource | A web tool for descriptive analysis of microarray data. The analysis is performed by looking for descriptions of gene sets that are statistically significantly over- or under-expressed between different scenarios within the context of a genome-scale experiments (DNA microarray). Descriptions are defined by using the terms from the Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and gene-gene interactions found in the ENTREZ database. Gene annotations by GO and KEGG terms can also be found in the ENTREZ database. The tool provides three procedures for testing the enrichment of the gene sets (over- or under-expressed): Fisher's exact test, GSEA and PAGE, and option for combining the results of the tests. Because of the multiple-hypothesis testing nature of the problem, all the p-values are computed using the permutation testing method. | microarray, pathway, gene-gene interaction, gene, interaction, annotation, gene expression, ortholog, molecular function, biological process, cellular component, enriched gene set, gene set |
is related to: Gene Ontology is related to: Entrez Gene is related to: KEGG is related to: GoMapMan has parent organization: Jozef Stefan Institute; Ljubljana; Slovenia |
PMID:18234563 | nlx_157688 | SCR_003554 | SciCrunch Registry | Search for Enriched Gene Sets | 2026-10-31 12:19:53 | 3 | |||||||
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ClueGO Resource Report Resource Website 1000+ mentions |
ClueGO (RRID:SCR_005748) | ClueGO | software resource | A Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. It can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be combined to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | statistical analysis, function, gene ontology, pathway, annotation, network, plugin, gene |
is listed by: Gene Ontology Tools is listed by: SoftCite is related to: Gene Ontology is related to: Cytoscape is related to: KEGG is related to: BioCarta Pathways has parent organization: National Institute of Health and Medical Research; Rennes; France |
National Institute of Health and Medical Research; Rennes; France ; Ville de Paris ; INCa ; Austrian Ministry for Science and Research ; BINII ; European Union 7FP 202230 |
PMID:19237447 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149209 | SCR_005748 | SciCrunch Registry | 2026-10-31 12:14:16 | 2951 | ||||||
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LegumeIP Resource Report Resource Website 10+ mentions |
LegumeIP (RRID:SCR_008906) | LegumeIP | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | LegumeIP is an integrative database and bioinformatics platform for comparative genomics and transcriptomics to facilitate the study of gene function and genome evolution in legumes, and ultimately to generate molecular based breeding tools to improve quality of crop legumes. LegumeIP currently hosts large-scale genomics and transcriptomics data, including: * Genomic sequences of three model legumes, i.e. Medicago truncatula, Glycine max (soybean) and Lotus japonicus, including two reference plant species, Arabidopsis thaliana and Poplar trichocarpa, with the annotation based on UniProt TrEMBL, InterProScan, Gene Ontology and KEGG databases. LegumeIP covers a total 222,217 protein-coding gene sequences. * Large-scale gene expression data compiled from 104 array hybridizations from L. japonicas, 156 array hybridizations from M. truncatula gene atlas database, and 14 RNA-Seq-based gene expression profiles from G. max on different tissues including four common tissues: Nodule, Flower, Root and Leaf. * Systematic synteny analysis among M. truncatula, G. max, L. japonicus and A. thaliana. * Reconstruction of gene family and gene family-wide phylogenetic analysis across the five hosted species. LegumeIP features comprehensive search and visualization tools to enable the flexible query on gene annotation, gene family, synteny, relative abundance of gene expression. | gene function, genome evolution, legume, gene, genome, plant, genomics, transcriptomic, gene annotation, gene family, synteny, gene expression, blast, genomic sequence, microarray, rna-seq, comparative genomics, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: UniProt is related to: InterProScan is related to: Gene Ontology is related to: KEGG has parent organization: Samuel Roberts Noble Foundation |
Samuel Roberts Noble Foundation ; NSF ABI-0960897 |
PMID:22110036 | biotools:legumeip, nlx_151455 | https://bio.tools/legumeip | SCR_008906 | SciCrunch Registry | LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes, LegumeIP - An Integrative Platform to Study Gene Function and Genome Evolution in Legumes | 2026-10-31 12:14:55 | 23 | |||||
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INMEX Resource Report Resource Website 10+ mentions |
INMEX (RRID:SCR_004173) | INMEX | analysis service resource, data analysis service, production service resource, service resource | A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner. | gene expression, meta-analysis, metabolomics, pathway, gene, metabolite, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: KEGG is related to: Human Metabolome Database has parent organization: University of British Columbia; British Columbia; Canada |
Killam Trust ; Canadian Institutes of Health Research |
PMID:23766290 | Acknowledgement requested | biotools:inmex, OMICS_01546 | https://bio.tools/inmex | SCR_004173 | SciCrunch Registry | INtegrative Meta-analysis of EXpression data, INMEX - INtegrative Meta-analysis of EXpression data | 2026-10-31 12:20:00 | 19 | ||||
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DIANA-mirPath Resource Report Resource Website 100+ mentions |
DIANA-mirPath (RRID:SCR_017354) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Pathway, analysis, statistics, assessment, miRNA, identify, regulatory, role, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Thessaly; Thessaly; Greece is provided by: DIANA Tools works with: KEGG works with: Gene Ontology |
Development Grants For Research Institutions – KRIPIS ; European Regional Development Fund ; European Social Fund ; General Secretariat for Research and Technology ; Ministry of Education ; Greece ; John S. Latsis Public Benefit Foundation |
PMID:25977294 PMID:19435746 PMID:22649059 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017495, biotools:diana-mirpath | http://diana.imis.athena-innovation.gr/DianaTools/, http://www.microrna.gr/miRPathv3, https://bio.tools/diana-mirpath | http://www.microrna.gr/miRPathv2 | SCR_017354 | SciCrunch Registry | miRPath, miRPathv3, miRPathv2, DIANA-miRPath v2.0, DIANA-miRPath v3.0 | 2026-10-31 12:16:51 | 424 | ||||
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FunNet - Transcriptional Networks Analysis Resource Report Resource Website 10+ mentions |
FunNet - Transcriptional Networks Analysis (RRID:SCR_006968) | FunNet | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource | Functional Analysis of Transcriptional Networks (FunNet) is designed as an integrative tool for analyzing gene co-expression networks built from microarray expression data. The analytical model implemented in this tool involves two abstraction layers: transcriptional (i.e. gene expression profiles) and functional (i.e. biological themes indicating the roles of the analyzed transcripts). A functional analysis technique, which relies on Gene Ontology and KEGG annotations, is applied to extract a list of relevant biological themes from microarray gene expression data. Afterwards multiple-instance representations are built to relate relevant biological themes to their annotated transcripts. An original non-linear dynamical model is used to quantify the contextual proximity of relevant genomic themes based on their patterns of propagation in the gene co-expression network (i.e. capturing the similarity of the expression profiles of the transcriptional instances of annotating themes). In the end an unsupervised multiple-instance spectral clustering procedure is used to explore the modular architecture of the co-expression network by grouping together biological themes demonstrating a significant relationship in the co-expression network. Functional and transcriptional representations of the co-expression network are provided, together with detailed information on the contextual centrality of related transcripts and genomic themes. FunNet is provided both as a web-based tool and as a standalone R package. The standalone R implementation can be run on any operating system for which an R environment implementation is available (Windows, Mac OS, various flavors of Linux and Unix) and can be downloaded from the FunNet website, or from the worldwide mirrors of CRAN. Both implementations of the FunNet tool are provided freely under the GNU General Public License 2.0. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | genome, transcriptional interaction, microarray, gene expression, statistical analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: KEGG has parent organization: Cordelier Research Center |
PMID:18208606 | Free for academic use, GNU General Public License, v2 | nlx_149243 | SCR_006968 | SciCrunch Registry | Functional Analysis of Transcriptional Networks, Functional Analysis of Transcriptional Networks (FunNet) | 2026-10-31 12:14:41 | 17 | ||||||
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OMICtools Resource Report Resource Website 10+ mentions |
OMICtools (RRID:SCR_002250) | OMICtools | catalog, data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis. | metadatabase, manually, curated, tool, genomic, transcriptomic, proteomic, metabolomic, data |
lists: ncdfFlow lists: BSmooth-align lists: 4Peaks lists: CSDeconv lists: Tablet lists: GenomicRanges lists: SNPSVM lists: ReadqPCR lists: SP-Designer lists: CorMut lists: ChIPmeta lists: FACS lists: metaSeq lists: Dissect lists: Fusion Analyser lists: FusionCatcher lists: GASV lists: GHOSTM lists: nFuse lists: PD5 lists: Patchwork lists: QuadGT lists: VariantAnnotation lists: ReQON lists: SnowsShoes-FTD lists: timecourse lists: SOAPfuse lists: SOAPfusion lists: pFind Studio: pLink lists: Spotfinder lists: AbMining ToolBox lists: SNAVI lists: MetAssign lists: JChemPaint lists: siRNArules lists: AutoPrime lists: RmiR.Hs.miRNA lists: MysiRNA-designer lists: TACOA lists: Treephyler lists: MedGen lists: D-Tailor lists: BioLemmatizer lists: AffyRNADegradation lists: Orphelia lists: ArrayExpress (R) lists: Parallel-META lists: CovalentDock Cloud lists: DOCK lists: exomeSuite lists: SPAdes lists: Sequence Read Format lists: FastQ Screen lists: GEOquery lists: Bovine Genome Database lists: GISTIC lists: DESeq lists: Postgwas lists: BLASTPLOT lists: miRanalyzer lists: Magnolya lists: GMATo lists: GemSIM lists: Grinder lists: Illuminate lists: RNAcontext lists: MIMOSA lists: F2DockClient lists: FlexX lists: Glide lists: GOLD lists: Molegro Virtual Docker lists: Sanjeevini lists: SODOCK lists: HEM lists: Surflex-Dock lists: Cascleave lists: MetaDE lists: Cell Death Proteomics Database lists: GPS-Calpain Cleavage Detector lists: GraBCas lists: c3net lists: Context Likelihood of Relatedness lists: GENIE3 lists: Inferelator lists: MODENT - A Tool For Reconstructing Gene Regulatory Networks lists: MRNet lists: UnSplicer lists: Duplicate reads removal lists: PEpiD lists: TAPIR: target prediction for plant microRNAs lists: iOMICS lists: Megraft lists: VARiD lists: Cistrome lists: PSGInfer lists: MochiView lists: RSEM lists: RNAmotifs lists: M(at)CBETH lists: MS-Spectre lists: Quant lists: RNASeqReadSimulator lists: iFad lists: GramCluster lists: GProX lists: PeptideProphet lists: CNTools lists: Lasergene's SeqMan Pro lists: ProteinProphet lists: OMSSAPercolator lists: Flicker lists: cn.FARMS lists: LIPAGE lists: DNASTAR: Lasergene Core Suite lists: Clonality lists: oneClickCGH lists: CGH Fusion lists: Screensaver lists: fqzcomp lists: ArrayPlex lists: MiRdup lists: MeQA lists: Methyl-Analyzer lists: Annotare lists: CpGassoc lists: Koadarray lists: RADtools lists: rtd lists: ABrowse lists: GPViz lists: cuteNMR lists: Jnomics lists: JMolDraw lists: CGAP-Align lists: ARACHNE lists: Kinannote lists: CLC Main Workbench lists: ParseCNV lists: TAPS lists: PyroHMMsnp lists: TransView lists: pvac lists: riboPicker lists: NucleoFinder lists: bzip2 lists: GENSENG lists: AS-Peak lists: is-rSNP lists: ILLUMINUS lists: QUALIFIER lists: FunctSNP lists: Micro-Analyzer lists: flowStats lists: flowPeaks lists: metaMA lists: rTANDEM lists: flowFlowJo lists: TargetCaller lists: PSCBS lists: iASeq lists: d2-tools lists: PEPPER lists: OLINgui lists: TNO-DECO lists: SigFuge lists: stsPlots lists: Sulfinator lists: Rdisop lists: pbcore lists: GeneExpressionSignature lists: sybil - Efficient Constrained Based Modelling in R lists: msbwt lists: MetaDrug lists: Reprever lists: POPBAM lists: SAMBLASTER lists: SpeedSeq lists: pyQPCR lists: RefFinder lists: PGS lists: miRprimer lists: iBMQ lists: NIMBL lists: TDARACNE lists: bamova lists: BAIT lists: ARNIE lists: fourSig lists: Mfuzz lists: MaryGold lists: TOPPAS lists: SPHINX lists: PhyloPythia lists: MATCHCLIP lists: mzMatch lists: Sequence Search and Alignment by Hashing Algorithm lists: ESPRIT lists: DySC lists: FPSAC lists: Scaffold builder lists: SNPiR lists: ACCUSA2 lists: MuTect lists: Pindel lists: rSeq lists: GERP lists: SiPhy lists: wANNOVAR lists: ViReMa lists: Smart Dictionary Lookup lists: VariantMaster lists: GeneWays lists: AdaptiveCrawler lists: NGS-Cleaner lists: flowQ lists: Database Enabled Code for Ideal Probe Hybridization Employing R lists: NGSmethPipe lists: Pyrocleaner lists: DecGPU lists: drFAST lists: MPscan lists: TAPyR lists: MutPred Splice lists: ContEst lists: Mini Analysis Guide for Microarrays lists: DDBJ Omics Archive lists: Chromas lists: OnEx - Ontology Evolution Explorer lists: BEBaC lists: FlipFlop lists: Phosphor Antibody Array Data Analysis lists: PhenoFam lists: forqs lists: GMcloser lists: GenomeWeb lists: Bycom lists: CorQ lists: NGS tools for the novice lists: Opera lists: SRMA lists: DeNovoGear lists: VarB lists: BAMseek lists: TriageTools lists: clipcrop lists: detecttd lists: FastUniq lists: GEUVADIS lists: TMAP lists: BISMA lists: FineSplice lists: RMAP lists: Sequencing Analysis Software lists: BLASR lists: GlycoWorkbench lists: jmzIdentML API lists: SciRoKo lists: HapCompass lists: JBrowse lists: DSRC lists: fastqz lists: GDC lists: GRS lists: PREFAB lists: BLASTP lists: Google Compute Engine lists: SplitSeek lists: ASC lists: NPEBseq lists: FUSIM lists: Geoffs Bio-Directories lists: Phred lists: MassGenomics lists: Illuminator lists: BAC lists: targetscan.Hs.eg.db lists: RmiR lists: MmPalateMiRNA lists: Starr lists: bsseq lists: Qvalue lists: ExomePeak lists: NextGenSeq(at)nature.com lists: AutoAssemblyD lists: CUDA-EC lists: rGADEM lists: qips lists: PICS lists: Jmosaics lists: SparseAssembler lists: BreakFusion lists: ParticleCall lists: DSGseq lists: R453Plus1Toolbox lists: SynView lists: ShortFuse lists: Cancer Gene Index lists: jmzML lists: CASVM lists: Birdseed lists: Reaper - Demultiplexing trimming and filtering sequencing data lists: GimmeMotifs lists: skewer lists: flowWorkspace lists: massiR lists: Transposon Insertion Finder lists: Shimmer lists: GenVision lists: DiMO lists: MetaPhyl lists: WiggleTools lists: EMI lists: SplicePlot lists: CrossMap lists: GraphIBD lists: rbsurv lists: Skylign lists: HMMvar lists: tbvar lists: STRViper lists: Breakway lists: Genometa lists: CATCHprofiles lists: VAAL lists: SLOPE lists: BreakSeq lists: Anchored Assembly lists: Bionimbus lists: ChIPMunk lists: RDPipeline lists: PeakAnalyzer lists: SomaticCall lists: Baa.pl lists: VirusHunter lists: seq2HLA lists: MUMmerGPU lists: GeneMeta lists: GenoMiner lists: GenoViewer lists: sim4cc lists: GenomicTools lists: Omixon Target HLA Typing lists: Omixon Target Data Analysis lists: PARalyzer lists: QualiMap lists: Lab7 lists: mlgt lists: BSSim lists: Golden Helix GenomeBrowse lists: HiPipe lists: MADAM lists: Microarray Data Analysis System lists: Automated Microarray Pipeline lists: MergeMaid lists: OmicsOffice for NGS SeqSolve lists: categoryCompare lists: metahdep lists: Plantagora lists: QUAST lists: TileQC lists: VectorFriends lists: vcflib lists: PHACCS lists: Sequedex lists: Genome Trax lists: VCFtools lists: NGSUtils lists: ChIP-seq lists: Tally lists: mapDamage lists: freeIbis lists: piCALL lists: ERGO lists: TALLYMER lists: KMC lists: DSK lists: Mutation Surveyor lists: BFCounter lists: snpStats: SnpMatrix and XSnpMatrix classes and methods lists: CNVtools lists: CGEN lists: RCASPAR lists: iterativeBMAsurv lists: multtest lists: globaltest lists: SABER lists: Local Ancestry in adMixed Populations lists: GemTools lists: MinimumDistance lists: ipPCA lists: ADMIXTURE lists: frappe lists: Mutascope lists: metabnorm lists: VegaMC lists: VanillaICE lists: SNPchip lists: SMAP lists: quantsmooth lists: mBPCR lists: ITALICS lists: GenoSet lists: exomeCopy lists: CGHregions lists: CGHbase lists: BlindCall lists: beadarraySNP lists: SSCprofiler lists: CGH-Explorer lists: GLAD lists: SNP and Variation Suite SNP Analysis lists: SNP and Variation Suite CNV Analysis lists: ProbRNA lists: methylMnM lists: methyAnalysis lists: les lists: ARRmNormalization lists: ChIPsim lists: Sherman lists: yaqcaffy lists: wateRmelon lists: sRAP lists: spotSegmentation lists: SNM lists: SNAGEE lists: Simpleaffy lists: qcmetrics lists: OLIN lists: MANOR lists: limmaGUI lists: ffpe lists: dyebias lists: DEXUS lists: BeadDataPackR lists: aroma.light lists: ArrayTools lists: beadarray lists: arrayQuality lists: arrayMvout lists: affyQCReport lists: affyPLM lists: affylmGUI lists: AffyExpress lists: waveTiling lists: KAnalyze lists: gprege lists: oneChannelGUI lists: CYCLE lists: LMGene lists: factDesign lists: pickgene lists: betr lists: NGSrich lists: SCAN.UPC lists: arrayQualityMetrics lists: CALIB lists: DEDS lists: Harshlight lists: MiChip lists: OCplus lists: bridge lists: FARMS lists: fRMA lists: genArise lists: lapmix lists: maCorrPlot lists: maSigPro lists: MACAT lists: maigesPack lists: MDQC lists: metaArray lists: nnNorm lists: plgem lists: PVCA lists: RAMA lists: stepNorm lists: virtualArray lists: LPE lists: DDBJ Sequence Read Archive lists: WegoLoc lists: Mugsy lists: Mspire-Simulator lists: CytoSPADE lists: vsn lists: ACME lists: GenGIS lists: CoGAPS lists: NTAP lists: ToppCluster lists: PyLOH lists: Nebula lists: Sequencher lists: flowFP lists: ChIPseeqer lists: CisGenome lists: CGHcall lists: rMAT lists: TileMap lists: Clustal Omega lists: BLASTN lists: SeqScape Software lists: BACContigEditor lists: Human Gene Mutation Database lists: AnimalTFDB lists: asSeq lists: Cuffdiff lists: BLASTX lists: SLqPCR lists: rSeqDiff lists: AffinDB lists: Enriched Domain Detector lists: A Classification of Mobile genetic Elements lists: PELICAN lists: nondetects lists: rlsim lists: Chilibot: Gene and Protein relationships from MEDLINE lists: unifiedWMWqPCR lists: HAPLOPAINTER lists: HOMOZYGOSITYMAPPER lists: QuasiSeq lists: sSeq lists: GERMLINE lists: MCMC.qpcr lists: CNVrd2 lists: TaLasso lists: pairedBayes lists: RNASeqBias lists: plateCore lists: PLINK lists: MACH 1.0 lists: PennSeq lists: FACTA+. lists: Prediction of Amyloid Structure Aggregation lists: TANGO lists: DNACLUST lists: InterMine lists: MSClust lists: ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets lists: RSVSim lists: TCC lists: SAMstrt lists: pRESTO lists: MEME Suite - Motif-based sequence analysis tools lists: PoissonSeq lists: CQN lists: GLiMMPS lists: TEMP lists: BEAGLE lists: SPP lists: BIRDSUITE lists: NASTIseq lists: BREAKDANCER lists: CAROL lists: COMPASS lists: CASAVA lists: flowClust lists: HSA lists: SPADE lists: AStalavista lists: Visual Molecular Dynamics lists: EXTREME lists: CYRILLIC lists: DINDEL lists: ASprofile lists: OrderedList lists: GenABEL lists: CCAT lists: Alt Event Finder lists: BroadPeak lists: SamSPECTRAL lists: THetA lists: TCW lists: GATK lists: Degust lists: flowUtils lists: DAVID lists: RchyOptimyx lists: StatAlign lists: Arabidopsis thaliana Protein Interactome Database lists: FGED lists: ExpressionPlot lists: S-MART lists: Pecan lists: SeqMonk lists: Ray lists: tbrowse lists: Bacteriome.org lists: Apollo lists: RAVEN lists: PEDIGRAPH lists: BAliBASE lists: TEQC lists: rSNPs MAPPER lists: rSNPBase lists: SNP Function Portal lists: flowType lists: SNPper lists: MADELINE lists: CanSNPer lists: ADaCGH2 lists: SGA lists: NormaCurve lists: GapMis lists: TRAMS lists: SNPMeta lists: SNPAAMapper lists: METAL lists: OLORIN lists: openADAM lists: SeqEM lists: SHARCGS lists: DMET-Analyzer lists: PEDHUNTER lists: AffyPipe lists: pSTIING lists: PTMcode lists: SHORTY lists: POLYMUTT lists: TissueNet - The Database of Human Tissue Protein-Protein Interactions lists: TRIP Database lists: SNVer lists: BISC lists: Primate Orthologous Exon Database lists: PurBayes lists: PyroHMMvar lists: flowViz lists: ChIPSeq Peak Finder lists: SpliceAid-F lists: Vennt lists: flowTrans lists: Spliceosome Database lists: cisRED: cis-regulatory element lists: ASPicDB lists: SAMTOOLS lists: HEXEvent lists: DBASS lists: FlyFactorSurvey lists: SNAP - SNP Annotation and Proxy Search lists: STIFDB lists: Cake lists: MPromDb lists: ProTISA lists: circlize lists: AmiGO lists: flowQB lists: Cinteny lists: RegPrecise lists: STRUCTURE lists: SVA lists: SYZYGY lists: TcoF lists: Matchprot lists: WebGeSTer DB lists: pfSNP lists: shinyTANDEM lists: CistromeMap lists: metaRNASeq lists: ZOOM lists: flowPlots lists: ImaGene lists: VAAST lists: ARACNE lists: FR-HIT lists: PROVEAN lists: flowPhyto lists: flowCore lists: flowMerge lists: RankAggreg lists: ConsensusPathDB lists: MAIA (Microarray Image Analysis) lists: CORUM lists: CoryneRegNet lists: miso-lims lists: COSMIC - Catalogue Of Somatic Mutations In Cancer lists: cpnDB: A Chaperonin Database lists: flowMap lists: rmeta lists: flowMeans lists: CTCFBSDB lists: spliceR lists: flowMatch lists: flowFit lists: DEMI lists: Binding MOAD lists: DBD: Transcription factor prediction database lists: CodonCodes TraceViewer lists: RelocaTE lists: MAGE lists: flowCyBar lists: Iterative Signature Algorithm lists: Variant Reporter Software lists: RepARK lists: PolyPhred lists: dbSNP lists: BEETL-fastq lists: DWGSIM lists: Ensembl lists: DBTBS lists: MIAME lists: MAQC lists: HaploClique lists: DBTSS: Database of Transcriptional Start Sites lists: DNA DataBank of Japan (DDBJ) lists: ISO lists: SBARS lists: Clinical and Laboratory Standards Institute lists: JGI Genome Portal lists: Cancer Genomics Consortium lists: BEAT lists: DOMINO: Domain peptide interactions lists: R Tutorial - An R Introduction to Statistics lists: R Tutorial lists: DOMINE: Database of Protein Interactions lists: GenomeSmasher lists: DOSY Toolbox lists: MUMA lists: Database of Rice Transcription Factors lists: VennDiagram lists: Quick-R lists: EcoCyc lists: Tree of Life lists: flowBeads lists: EDAS - EST-Derived Alternative Splicing Database lists: eggNOG lists: NRDR lists: YLoc lists: CAMERA - Collection of annotation related methods for mass spectrometry data lists: EID: Exon-Intron Database lists: WoLF PSORT lists: Entrez Gene lists: Mason lists: QualitySNPng lists: EPDnew lists: realSFS lists: pymzML lists: RUbioSeq lists: PBSIM lists: PennCNV lists: pIRS lists: PeptideShaker lists: ShotGun lists: Gibbs Motif Sampler lists: Zebrafish Information Network (ZFIN) lists: Wessim lists: BioStar lists: MBASED lists: discoSnp lists: RVD lists: SEEK lists: MethylAid lists: ExomeDepth lists: libmgf lists: Autophagy Database lists: T3DB lists: RopeBWT2 lists: e-Driver lists: sapFinder lists: PharmGKB lists: CTF lists: SuperTarget lists: DrugBank lists: PANDAseq lists: NCBI database of Genotypes and Phenotypes (dbGap) lists: leeHom lists: Reflect lists: Mapix lists: Rainbow lists: CASBAH lists: TelSeq lists: Pathview lists: GLProbs lists: rBiopaxParser lists: DSS lists: GATE lists: NetPathMiner lists: NMR metabolomics database of Linkoping lists: GenBank lists: HINT lists: libCSAM lists: RNA Abundance Database lists: GeneCards lists: BINOCh lists: AliView lists: TherMos lists: ANDES lists: PacmonSTR lists: RMassBank lists: FisHiCal lists: Mutation Annotation and Genomic Interpretation lists: Circleator lists: IMEx - The International Molecular Exchange Consortium lists: Batch Oligo Selection Script lists: iontree lists: MicroVigene lists: Greengenes lists: Basic4Cseq lists: rDock lists: hot scan lists: International HapMap Project lists: BiGGR lists: mzR lists: PAPi lists: pNovo+ lists: COV2HTML lists: CODEHOP lists: CNVassoc lists: PRO lists: Hollywood lists: StreamingTrim lists: pLabel lists: HomoloGene lists: aCGH.Spline lists: pBuild lists: Time-series RNA-seq Analysis Package lists: CGHnormaliter lists: Type-III-Secretion-System related database lists: SMRT-Analysis lists: CPTRA lists: mtDB - Human Mitochondrial Genome Database lists: AltAnalyze - Alternative Splicing Analysis Tool lists: Chimera lists: IMG System lists: Babelomics lists: MRFSEQ lists: ms lims lists: ChIPMonk lists: Gel2DE lists: UCSF Spot lists: ProRata lists: R-pbutils lists: MITOMAP - A human mitochondrial genome database lists: NOISeq lists: Dpos lists: Gene Weaver lists: pFind lists: Canadian College of Medical Geneticists lists: BRAIN lists: Isopat lists: R-pbh5 lists: pbh5tools lists: SMRT View lists: JASPAR lists: enviPat lists: bwtool lists: MoSDi lists: tweeDEseq lists: DIALIGN lists: PacBioToCA lists: DiNuP lists: Gutentag lists: Parametric Time Warping lists: SurvComp lists: SASqPCR lists: enviPick lists: GeneFisher lists: Triplex lists: MPprimer lists: MIPE lists: MFEprimer lists: DnaSP lists: FAS-DPD lists: SURPI lists: MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation lists: MachiBase lists: Primer3Plus lists: e-PCR lists: NeuroMab lists: In-Silico PCR lists: JETTA lists: MapViewer lists: Primer-BLAST lists: WormBase lists: eQtlBma lists: JuncBASE lists: MethDB lists: pairheatmap lists: MISO lists: HYDEN lists: mrsFAST lists: PredictNLS lists: mrCaNaVaR lists: NovelSeq lists: PlantLoc lists: Primer3 lists: FastSNP lists: Proteome Analyst Specialized Subcellular Localization Server lists: NYCE lists: GeneScissors lists: ngLOC lists: MultiLoc lists: GeneCruiser lists: MetaLocGramN lists: FastPCR lists: miRNAMap lists: HUPO Proteomics Standards Initiative lists: SaskPrimerFS lists: rDiff lists: Database of Interacting Proteins (DIP) lists: Solas lists: Pipeliner lists: iLoc-Animal lists: QDNAseq lists: ResponseNet lists: SynSysNet lists: XORRO lists: Stacks lists: SECISearch3 and Seblastian lists: SALT lists: HyperTree lists: Primer Designer lists: r3Cseq lists: Gene Set Enrichment Analysis lists: Piano lists: PHAST lists: NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects lists: NGSadmix lists: Gemi lists: Talking Glossary of Genetic Terms lists: PathGuide: the pathway resource list lists: SplicingCompass lists: RNAhybrid lists: LUMPY lists: Geospiza lists: SpliCQ lists: ORFprimer lists: JCVI Primer Designer lists: Assembly Based ReAligner lists: deFuse lists: Xenbase lists: PoPoolation2 lists: OmicCircos lists: Amplicon lists: PrimerSeq lists: Genedata Expressionist lists: biobambam lists: RCircos lists: ggbio lists: DAFGA lists: MIPgen lists: PicTar lists: BlockClust lists: PIRSF lists: miR-PREFeR lists: MouseNET lists: PlantProm DB lists: MAGI lists: PLANTTFDB lists: ALDEx2 lists: qBasePLUS lists: RefGenes lists: HTqPCR lists: BestKeeper lists: NanoStringNorm lists: NormFinder lists: NormqPCR lists: PolymiRTS lists: PPDB: Plant Promoter Database lists: ddCt lists: GEOSS lists: PReMod lists: EasyqpcR lists: NanoStriDE lists: GBSA lists: LaSSO lists: NAPPA lists: nSolver Analysis Software lists: MAGENTA lists: MetABEL lists: ProNIT lists: genomation lists: metagen lists: BMIQ lists: FadE lists: metaphor lists: SWAN lists: PROSITE lists: Parseq lists: qPrimerDepot lists: Bpipe lists: Nestly lists: Snakemake lists: SNAPE-pooled lists: NGSANE lists: jmzTab lists: JISTIC lists: Savant lists: MetaSKAT lists: Human Variome Project lists: PoPoolation lists: RefSeq lists: MultiPhen lists: RegulonDB lists: MF-GE lists: PheWAS R Package lists: EBSeq lists: MSMS lists: RAREMETAL lists: RevMan lists: GEPAT lists: Polyester lists: SET lists: J-Express lists: UEA sRNA toolkit lists: Osprey lists: RINS lists: PyroBayes lists: PEAR lists: JATAC lists: SeqExpress lists: Quantitative Enrichment of Sequence Tags lists: Pash 3.0 lists: Factorbook lists: FlyTF.org lists: My Cancer Genome lists: Pathosystems Resource Integration Center lists: MSG lists: InsertionMapper lists: PubMed Central lists: GeneCommittee lists: INMEX lists: TagDust lists: PASS-bis lists: HLASeq lists: FIDEA lists: EGAPP lists: DCTD lists: Hapmix lists: BamView lists: PerM lists: Mercury lists: CDP lists: CB-Commander lists: BSRD lists: DER Finder lists: Artemis: Genome Browser and Annotation Tool lists: PeaKDEck lists: PubChem lists: Babel lists: bcbio-nextgen lists: SIDER lists: EpiGRAPH lists: DRUT lists: Ancestrymap lists: VIROME lists: Vanator lists: FACIL lists: Velvet-SC lists: SNiPer-HD lists: Squeezambler lists: UniGene lists: SCPD - Saccharomyces cerevisiae promoter database lists: GASSST lists: SnoopCGH lists: Taverna lists: PASHA lists: miRDeepFinder lists: STAR lists: Spanki lists: VAMPS lists: Basic OligoNucleotide Design lists: Tree and reticulogram REConstruction lists: ACT: Artemis Comparison Tool lists: SPInDel lists: Kdetrees lists: tree editor lists: Genomedata lists: BioDiscovery Nexus Copy Number lists: TETRA lists: MetaCluster-TA lists: DELLY lists: QuickGO lists: TAIR lists: CompostBin lists: Nonpareil lists: BioPig lists: LMAT lists: AbundanceBin lists: TaxSOM lists: NuChart lists: ProViDE lists: UnifiedGenotyper lists: SOrt-ITEMS lists: RAIphy lists: Human DNA Polymerase Gamma Mutation Database lists: Pfam lists: Distributed String Mining Framework lists: Pplacer lists: deStruct lists: Phymm and PhymmBL lists: USeq lists: NucPosSimulator lists: NBC lists: SVMerge lists: MLTreeMap lists: SVseq lists: SEQanswers lists: PRISM - Pair Read Informed Split Mapper lists: miRNAKey lists: MG-RAST lists: Information Hyperlinked Over Proteins lists: PubMed lists: MetaPhyler lists: MARTA lists: NCBI BioSample lists: BioSample Database at EBI lists: DiScRIBinATE lists: VariationHunter lists: NCBI BLAST lists: IBIS: Inferred Biomolecular Interactions Server lists: NCBI Sequence Read Archive (SRA) lists: MetaPhlAn lists: Classifier for Metagenomic Sequences lists: MapAl lists: European Genome phenome Archive lists: TemplateFilter lists: Minia lists: MiTCR lists: M-pick lists: CARMA lists: SLIQ lists: DNAPlotter lists: AmphoraNet lists: UPARSE lists: SOPRA lists: ESPRIT-Tree lists: HPC-CLUST lists: mirWIP lists: SSPACE lists: GoMapMan lists: G-BLASTN lists: SINA lists: Bambus lists: AGORA lists: GRASS lists: MIP Scaffolder lists: Scarpa lists: MBCluster.Seq lists: cortex var lists: Flux Simulator lists: BEERS lists: SNPeffect lists: MMAPPR lists: Cloudbreak lists: comrad lists: qSNP lists: SomaticIndelDetector lists: SomaticSniper lists: aldex lists: UnoSeq lists: Traph lists: RNA-SeQC lists: PoPoolation TE lists: RetroSeq lists: T-lex lists: SLIDE lists: VFS lists: Project HOPE lists: PANTHER Evolutionary analysis of coding SNPs lists: rQuant lists: Naturejobs lists: jobs.ac.uk lists: ASOoViR lists: RNA-eXpress lists: MethPipe lists: AnnTools lists: AVIA lists: CandiSNPer lists: CHAoS lists: COVA lists: methylKit lists: dbNSFP lists: GESND lists: VAGrENT lists: Human Splicing Finder lists: NGS-SNP lists: Oncotator lists: PHAge Search Tool lists: SCAN lists: SeqAnt lists: SNPdat lists: ORMAN lists: FRCbam lists: SNPdbe lists: SnpEff lists: SNPnexus lists: SPOT - Biological prioritization after a SNP association study lists: VARIANT lists: ABSOLUTE lists: ExPANdS lists: HIVCD lists: PathSeq lists: READSCAN lists: VirusFinder lists: VirusSeq lists: PredictHaplo lists: QuRe lists: ShoRAH lists: V-Phaser 2 lists: NSMAP lists: FlowSim lists: SimRare lists: SAMtools/BCFtools lists: MiTie lists: GeneTalk lists: iReckon lists: Genomic Datasharing lists: IsoformEx lists: IQSeq lists: ERANGE lists: FusionMap lists: Bioinformatics(at)school lists: PhenoMan lists: Models of SHM Targeting and Substitution lists: AGE lists: Breakpointer lists: CLEVER Toolkit lists: Clippers lists: CREST lists: Indelocator lists: GASVPro lists: Hydra lists: inGAP lists: VelociMapper lists: PEMer lists: SPLITREAD lists: SpliceSeq lists: Scripture lists: Omicsoft Sequence Aligner lists: SOAPindel lists: G-Mo.R-Se lists: SEECER lists: RSeQC lists: SeqWare lists: CloVR lists: PolySearch lists: MiRPara lists: PIE the search lists: miRdSNP lists: Hmmer lists: MuGeX lists: SysCall lists: KGGSeq lists: MycoCosm lists: EBIMed lists: HighWire lists: Coremine Medical lists: Assembly Likelihood Estimator lists: CoPub lists: ABS filter lists: NCBO Annotator lists: CHANCE lists: phantompeakqualtools lists: CoIN lists: SwissRegulon lists: becas lists: GEM lists: Anne O'Tate lists: (at)Note lists: PeakSeq lists: FaBox lists: CoverageCalculator lists: Spliceman lists: Yabi lists: footprintDB lists: MolBioLib lists: Moa lists: PRISM (Stanford database) lists: Knime4Bio lists: Ergatis lists: bioKepler lists: Platypus lists: PING lists: Binding and Expression Target Analysis lists: BioExtract lists: Bio-Linux lists: NeuroLex lists: ChEA lists: ChIPBase lists: CistromeFinder lists: pyDNase lists: hmChIP lists: HOCOMOCO lists: PAZAR lists: TFinDIT lists: AtProbe lists: DATFAP lists: StSNP lists: SolexaQA lists: TOBFAC lists: MapNext lists: BSeQC lists: SKIPPY lists: SAMStat lists: QC-Chain lists: Bis-SNP lists: Bisulfighter lists: CpG MPs lists: CyMATE lists: GobyWeb lists: Kismeth lists: MethylExtract lists: MethylViewer lists: MLML lists: MSC lists: PRINSEQ lists: NGSQC lists: NGS QC Toolkit lists: NextClip lists: Geneious Microsatellite Plugin lists: DistMap lists: PRIMEGENS lists: VDJ lists: Bowtie lists: CASHX lists: CUSHAW lists: CUSHAW2-GPU lists: GNUMAP lists: GSNAP lists: Kraken lists: Maq lists: MOSAIK lists: mrFAST lists: NextGenMap lists: ngsTools lists: PASS lists: Jellyfish lists: TIGRFAMS lists: Segemehl lists: SeqMap lists: SHRiMP lists: WHAM lists: SMALT lists: Scalable Nucleotide Alignment Program lists: SOAP3 lists: SOAPaligner/soap2 lists: Stampy lists: TreQ lists: IdCheck lists: HTSeq lists: Hadoop-BAM lists: MACE lists: Fulcrum lists: FreClu lists: FLASH lists: FASTX-Toolkit lists: Hiclib lists: FastQC lists: cd-hit-454 lists: CGAT lists: ea-utils lists: Genetic Testing Registry lists: Ridom TraceEdit lists: HiCUP lists: TopoSNP lists: TM4 lists: WebArrayDB lists: Advanced Sequence Automated Pipeline lists: Unipro UGENE lists: SeqTrace lists: MethylomeDB lists: FinchTV lists: DNA Chromatogram Explorer lists: Chromaseq lists: OXBench lists: Sybil lists: cancergrid-tma lists: PathXL TMA lists: Slidepath lists: Stanford TMA Software lists: TMA Navigator lists: TMA-Combiner lists: TMAJ lists: X-Tile lists: Bismark lists: jMHC lists: VAGUE lists: Tractor db lists: SAMtools Text Alignment Viewer lists: snp-search lists: TRANSFAC lists: Systems Transcriptional Activity Reconstruction lists: SPOT lists: LookSeq lists: Staden Package lists: Maqview lists: NGSView lists: BS Seeker lists: WISECONDOR lists: MagicViewer lists: Bambino lists: Consed lists: DiProGB lists: BSMAP lists: netClass lists: BSmooth lists: DMRforPairs lists: SeqGSEA lists: CLIPZ lists: PePr lists: MutationAssessor lists: American College of Medical Genetics and Genomics lists: Biopieces lists: SNPsandGO lists: Unified Human Interactome lists: OLego lists: PIPE-CLIP lists: GoPubMed lists: SPLINTER lists: GraphProt lists: Cascade lists: PASSion lists: JEPETTO lists: dna-bison lists: aLFQ lists: BLESS lists: VirHostNet: Virus-Host Network lists: CAFE lists: VirusMINT lists: GNUMAP-BS lists: MetaQC lists: YuGene lists: h5vc lists: IQRray lists: Yeast Search for Transcriptional Regulators And Consensus Tracking lists: LAST lists: ScerTF lists: Tangram lists: ClinVar lists: estMOI lists: FCROS lists: WashU Epigenome Browser lists: deepSNV lists: OMPdb lists: Rosalind lists: pepStat lists: PANOGA lists: InterSpecies Analysing Application using Containers lists: GeneTrail lists: MEDIE lists: DBM-DB lists: SpliceDB lists: RUVSeq lists: Genomic Standards Consortium lists: Galaxy lists: VICUNA lists: Lists2Networks lists: PredictSNP lists: ADGO lists: KOBAS lists: GeneTerm Linker lists: Computational Genomics Analysis Tools lists: Antibody Registry lists: BHC lists: Wigwams lists: BETASEQ lists: PhyloBayes lists: MEGA-MD lists: CGARS lists: Magic lists: epigenomix lists: QCGWAS lists: AbsCN-seq lists: DupRecover lists: Socrates lists: CMGRN lists: SNPdryad lists: ALEA lists: MSIsensor lists: TSSer lists: IRanges lists: SILVA lists: kFM-index lists: Bioconductor lists: CHASM/SNV-Box lists: HTQC lists: GeneNetworkBuilder lists: Jalview lists: SV-M lists: Hereditary Hearing Loss Homepage lists: ATRHUNTER lists: seq crumbs lists: Google App Engine lists: COHCAP lists: MethylSeekR lists: SAAP-RRBS lists: targetHub lists: SRAdb lists: Picard lists: NGS-QC Generator lists: ART lists: HOMSTRAD - Homologous Structure Alignment Database lists: DECIPHER lists: GeneReviews lists: GigaScience lists: Leiden Open Variation Database lists: DGIdb lists: casper lists: htSeqTools lists: GWAMA lists: Orphanet lists: Ribosomal Database Project lists: DroID - Drosophila Interactions Database lists: BEDTools lists: PROGENY lists: APOLLOH lists: TIGAR lists: FLUX CAPACITOR lists: ChIPXpress lists: SpliceGrapher lists: waviCGH lists: Rice Genome Annotation lists: DMEAS lists: SoftSearch lists: SToRM lists: ALEXA-Seq lists: methVisual lists: DeconRNASeq lists: Samscope lists: AthaMap lists: SpliceTrap lists: Consensus CDS lists: GARM lists: Decombinator lists: FDM lists: fitGCP lists: EDASeq lists: Cscan lists: Next-gen Sequencing Scaffolding Tool lists: geNORM lists: GASiC lists: Ensembl Genomes lists: Qudaich lists: Nex-StoCT lists: Virmid lists: BIGpre lists: mubiomics lists: REDfly Regulatory Element Database for Drosophilia lists: EBCall lists: ENCODE lists: GBS barcode splitter lists: Sickle lists: JointSNVMix lists: RIPSeeker lists: ShortRead lists: TaxoAssignement lists: mutationSeq lists: QUASR lists: simhtsd lists: 1000 Genomes: A Deep Catalog of Human Genetic Variation lists: GBrowse lists: seqbias lists: EagleView lists: HIA lists: qrqc lists: Genomes Unzipped lists: eXpress lists: ArtificialFastqGenerator lists: BarraCUDA lists: RazerS lists: Therapeutic Target Database lists: YeTFaSCo lists: PrimerBank lists: MORGAN lists: CROP lists: MeDUSA lists: Arabidopsis Gene Regulatory Information Server lists: SimSeq lists: MetMap lists: MIGen lists: eDMR lists: ProDom lists: BAMStats lists: CD-HIT-OTU lists: microRNA.org lists: Database of Genomic Variants lists: DeconSeq lists: Psort lists: Kinetic Data of Bio-molecular Interaction lists: PRODORIC lists: Database of Poplar Transcription Factors lists: BioRAT lists: Database of Arabidopsis Transcription Factors lists: RTPrimerDB- The Real-Time PCR and Probe Database lists: Pripper lists: COG lists: Yeast Intron Database lists: QDMR lists: Haldanes Sieve lists: Kevin's GATTACA World lists: Next-Gen Sequencing lists: Public Expression Profiling Resource lists: EpiExplorer lists: swDMR lists: SEURAT lists: EVORA lists: Taipan lists: GEB lists: YM500 lists: peakrots lists: Peakzilla lists: ECgene: Gene Modeling with Alternative Splicing lists: polyaPeak lists: RSEG lists: BigWig and BigBed lists: DriverDB lists: NECTAR lists: miRGator lists: BRIG lists: AmpliconNoise lists: HilbertVis lists: Variant Effect Predictor lists: GenoTan lists: Search Tool for Interactions of Chemicals lists: HighSSR lists: YHap lists: INVERTER lists: Annotation-Modules lists: lobSTR lists: BiQAnalyzer HT lists: UCHIME lists: ActiveDriver lists: MMSEQ lists: Anno-J lists: DADA lists: CanPredict lists: QIIME lists: OnlineCall lists: Seven Bridges Genomics lists: ChroMoS lists: Gene Array Analyzer lists: IsaCGH lists: RJaCGH lists: CAT lists: Ultrasome lists: DEGseq lists: World Health Organization lists: FoldX lists: VAMP lists: OMICS! OMICS! lists: SeqPig lists: Condel lists: DMI lists: DARIO lists: DrGaP lists: eXtasy lists: Tute Genomics lists: Exon Array Analyzer lists: Biodoop lists: OligoPicker lists: InVEx lists: Textpresso lists: YunBe lists: DWD lists: PASTA lists: isva lists: QPALMA lists: MuSiC lists: svd lists: QuasiRecomb lists: RUM lists: XPN lists: Sequgio lists: ExpressYourself lists: FGDP lists: DELIMINATE lists: GAAS lists: Gecko lists: DNAzip lists: CMAP lists: SeqSaw lists: GReEn lists: Gzip lists: MFCompress lists: NGC lists: Quip lists: SIMHAP lists: CPSS lists: RLZ lists: A sample size calculation method lists: iMir lists: isomiRex lists: ISRNA lists: SeqBuster lists: shortran lists: SpliceMap lists: Generic Exome Analysis Plan lists: SCALCE lists: mirTools lists: Subread lists: isomiRID lists: Supersplat lists: TrueSight lists: RNASEQR lists: MicroSNiPer lists: BitSeq lists: MSbind lists: CLIIQ lists: IsoEM lists: Omixon blog lists: RNA-Seq Blog lists: AllSeq lists: ABMapper lists: EULER-SR lists: ContextMap lists: Geneious lists: TargetMiner lists: SOAPsnp lists: Gossamer lists: CRAC lists: JR-Assembler lists: vipR lists: MaSuRCA lists: Meraculous lists: ABySS lists: MIRA lists: PE-Assembler lists: QSRA lists: ALLPATHS-LG lists: IMGT/V-QUEST lists: Celera assembler lists: CloudBrush lists: SOAPdenovo lists: SSAKE lists: SUTTA lists: Velvet lists: Atlas2 lists: ComB lists: CopySeq lists: CRISP lists: FamSeq lists: FreeBayes lists: GAMES lists: glfMultiples lists: MoDIL lists: MISA lists: SSRLocator lists: SSR pipeline lists: T-REKS lists: TRhist lists: AgileVariantMapper lists: HomSI lists: Align-GVGD lists: CUPSAT lists: LS-SNP/PDB lists: MAPP lists: mCSM lists: MutationTaster lists: MutPred lists: MutSig lists: nsSNPAnalyzer lists: Oncodrive-fm lists: PhD-SNP lists: PMut lists: PriVar lists: SAPRED lists: SNAP - Effects of Single Amino Acid Substitutions on Protein Function lists: SNPs3D lists: TransFIC lists: Diplotyper lists: EMINIM lists: HapCUT lists: HARSH lists: HapFABIA lists: Relate lists: Pedigree-Draw lists: Pedimap lists: Phylogeny Programs lists: NHLBI Grand Opportunity Exome Sequencing Project lists: PhenCode lists: SNP and indel Imputability lists: draw-sneakpeek lists: GensearchNGS lists: HugeSeq lists: MutFinder lists: RTG Variant lists: reseqtools lists: SIMPLEX lists: TREAT lists: WEP lists: breseq lists: SVDetect lists: CEQer lists: CONTRA lists: ExomeCNV lists: CNAnorm lists: CNAseg lists: CnD lists: CNValidator lists: CNVer lists: CNVnator lists: Control-FREEC lists: JointSLM lists: readDepth lists: rSW-seq lists: SegSeq lists: CoRAL - Classification of RNAs by Analysis of Length lists: miRDeep lists: miREval lists: miRExpress lists: miRspring lists: omiRas lists: ShortStack lists: tRNAscan-SE lists: RNAsnp lists: BCmicrO lists: C-mii lists: DIANA-LncBase lists: TarBase lists: HOCTAR lists: SICER lists: MapSplice lists: TargetScan lists: MicroCosm Targets lists: MicroMUMMIE lists: miRDB lists: miRNA lists: miRNAminer lists: miRTar lists: COPS lists: PITA lists: PMTED lists: dPeak lists: E-RANGE lists: FindPeaks lists: HMCan lists: HPeak lists: MICSA lists: MOSAiCS lists: NEXT-peak lists: PeakRanger lists: RRBSMAP lists: SIPeS lists: SISSRs lists: T-PIC lists: ZINBA lists: MAnorm lists: POLYPHEMUS lists: ChIPDiff Library Comparison lists: DBChIP lists: diffReps lists: DIME lists: AlignACE lists: Arpeggio lists: ChIPModule lists: CompleteMOTIFs lists: diChIPMunk lists: F-Seq lists: HOMER lists: kmer-SVM lists: LASAGNA-Search lists: oPOSSUM lists: Pscan-ChIP lists: RSAT peak-motifs lists: TFBSGroup lists: TFFM lists: NOrMAL lists: NPS lists: NSeq lists: Nu-OSCAR lists: NucDe lists: NucHunter lists: nucleR lists: LegumeTFDB lists: PlanTAPDB lists: PlantTFcat lists: PlnTFDB lists: SoyDB lists: TreeTFDB lists: mCarts lists: Piranha lists: MeRIP-PF lists: B-SOLANA lists: BatMeth lists: QUMA lists: MethMarker lists: Genomic HyperBrowser lists: BWA lists: CloudBurst lists: ERNE lists: PPSEQ lists: SEAL lists: aCGHtool lists: ADaCGH lists: Agilent CytoGenomics software lists: Agilent Genomic Workbench lists: Aroma.affymetrix lists: CGH Explorer lists: CGHPRO lists: CGHseg lists: CGHweb lists: CNA-HMMer lists: CNVPartition lists: CytoSure Interpret Software lists: FISH Oracle lists: GenoSNP lists: Genotyping Console Software lists: Genovar lists: Ginkgo lists: ArrayAnalysis.org lists: arrayMagic lists: ArrayPipe lists: ArrayQuest lists: Asterias lists: BASE lists: BRB-ArrayTools lists: Chipster lists: EMMA2 lists: XDrawChem lists: LCB-DWH lists: LIMMA lists: M-CHiPS lists: Mayday lists: CEAS lists: CoCo lists: NIA Array Analysis lists: Oncomine lists: RACE lists: SAM lists: miRCURY LNA microRNA Array Analysis Software lists: BioTile lists: FastDMA lists: IMA lists: Marmal-aid lists: MethLAB lists: RnBeads lists: RPPanalyzer lists: Array Designer lists: OligoArray lists: OligoFaktory lists: Picky lists: ProbeMaker lists: PROBEmer lists: ProDesign lists: ROSO lists: balony lists: GenePix Pro lists: BxArrays lists: GeneSpring GX lists: GenomeStudio lists: ComBat lists: Genopolis lists: MicroGen lists: MUSC DNA Microarray Database lists: TAD lists: UNC Microarray Database lists: ABySS-Explorer lists: DNPTrapper lists: Hawkeye lists: NURD lists: European Medicines Agency lists: PALMapper lists: Argo Genome Browser lists: CGView lists: Gaggle lists: Annmap lists: Genome Projector lists: Genomicus lists: IGB lists: Integrative Genomics Viewer lists: NCBI Genome Workbench lists: ngs.plot lists: UCSC Cancer Genomics Browser lists: UTGB Toolkit lists: Circos lists: G-compass lists: GenomeMatcher lists: GenomeRing lists: Gobe lists: GSV lists: MizBee lists: GNomEx lists: PipMaker and MultiPipMaker lists: SynBrowse lists: VISTA Browser lists: Infernal lists: Kalign lists: MAFFT lists: MUSCLE lists: ProbCons lists: PSAR-Align lists: openBIS lists: PiMS lists: SABmark lists: T-Coffee lists: FASTA lists: GPU-BLAST lists: PatMaN lists: TBLASTN lists: TBLASTX lists: WU-BLAST lists: Hammer lists: HiTEC lists: B-Fabric lists: BIKA lists: Galaxy LIMS lists: SBEAMS lists: discovering-cse lists: MT-Toolbox lists: AdapterRemoval lists: AlienTrimmer lists: Btrim lists: CANGS lists: ConDeTri lists: Quake lists: QuorUM lists: cutadapt lists: QTrim lists: sabre lists: Scythe lists: SeqtrimNEXT lists: TagCleaner lists: Trim Galore lists: Trimmomatic lists: Coral lists: DecGPU lists: ECHO lists: RACER lists: CLC Genomics Workbench lists: DNASTAR: Lasergene Genomics Suite lists: Genomatix Solutions lists: SNP and Variation Suite lists: JMP Genomics lists: NARWHAL lists: NextGENe lists: Partek Genomics Suite lists: SeqGene lists: SeqPipe lists: SHORE lists: Genboree Workbench lists: Ibis lists: naiveBayesCall lists: htseq-count lists: ABNER lists: BioCaster lists: LitInspector lists: RefMED lists: Eucalyptus lists: HP Public Cloud lists: Joyent lists: Rackspace lists: VirtualBox lists: BBSeq lists: VMware lists: Apache Hadoop lists: Windows Azure lists: BaseSpace lists: BioVLAB lists: CloudBioLinux lists: DNAnexus lists: Genestack lists: GenomeCloud lists: Globus Genomics lists: Scotty lists: EBARDenovo lists: IDBA-Tran lists: IsoInfer lists: KisSplice lists: FusionFinder lists: FusionHunter lists: Oases lists: Rnnotator lists: STM lists: TopHat-Fusion lists: RNAseqViewer lists: Eoulsan lists: FX lists: Guide lists: Oncofuse lists: Oqtans lists: PRADA lists: R-SAP lists: RobiNA lists: RseqFlow lists: GeneStitch lists: Genovo lists: IDBA-UD lists: Meta-IDBA lists: MetAMOS lists: MetaVelvet lists: Newbler lists: Phrap lists: Ray Meta lists: BLAT lists: Mega BLAST lists: UCLUST algorithm lists: eXPatGen lists: PhyloPythiaS lists: CAMERA lists: CoMet lists: METAREP lists: RAMMCAP lists: FGENESH lists: FragGeneScan lists: GeneMark lists: Glimmer lists: Glimmer-MG lists: HMMgene lists: MetaGeneAnnotator lists: MGC lists: Prodigal lists: Explicet lists: MetaSee lists: SynTView lists: MetaSim lists: NeSSM lists: MEGAN lists: MOCAT lists: pyGCluster lists: CancerResource lists: ARTIVA lists: mothur lists: QIIME lists: RTG Metagenomics lists: vegan lists: WebMGA lists: PTP lists: GeneTack lists: JiffyNet lists: ArrayMiner lists: Genomics of Drug Sensitivity in Cancer lists: SuperCYP lists: AutoDock Vina lists: CGDB lists: Potassium Channel Database lists: Orientations of Proteins in Membranes database lists: PDBTM lists: PREDDIMER lists: TMDET lists: BaCelLo lists: Cell-PLoc lists: INSDC lists: CELLO lists: ClubSub-P lists: CoBaltDB lists: Euk-mPLoc lists: HSLPred lists: iLoc-Plant lists: KnowPredsite lists: University of Pittsburgh, Health Sciences Library System lists: CaMPDB lists: TIGRESS lists: OMA Browser lists: orthAgogue lists: OrthoDB lists: QuartetS-DB lists: NGS Leaders lists: reddit lists: Stack Overflow lists: CoreGenomics lists: Bio-IT World lists: Bioinformatics.fr lists: Bioinformaticsweb lists: Getting Genetics Done lists: SIOMICS lists: HTS Mappers lists: Microarrays.org lists: Next Generation Sequencing WikiBook lists: 1DegreeBio lists: Antibody Portal lists: Antibody Validation Database lists: Biocompare Antibody Search Tool lists: AACC lists: APHA lists: APHL lists: FABIA lists: BiBench lists: ExpressionView lists: COALESCE lists: Gene ARMADA lists: GenoREAD lists: Bioinformatics Organization lists: International Society for Computational Biology lists: BioSpace lists: My Biomedical Informatics Blog lists: Bits and Bugs lists: Cancer Methylome System lists: DBCAT lists: Histone Systematic Mutation Database lists: Genome Alteration Print lists: methPrimerDB lists: TFClass lists: APPRIS lists: easyRNASeq lists: TSPM.R lists: ShrinkSeq lists: Syapse lists: VisSR lists: Standalone hamming lists: GenomeJack lists: digitagCT lists: CCAT (Combinatorial Code Analysis Tool) lists: GPU-Meta-Storms lists: AnalyzeReplication lists: DIYABC lists: FamAnn lists: GARNET lists: Algal Functional Annotation Tool lists: gsGator lists: Scramble lists: FiGS lists: PerlPrimer lists: CowCoDA lists: MZmine lists: OBI-Warp lists: CPFP lists: TOPP lists: swissPIT lists: Antilope lists: ICPL ESIQuant lists: MetExtract lists: MFPaQ lists: jmzReader lists: PRIDE Converter 2 lists: Pride-asap lists: thermo-msf-parser lists: SearchGUI lists: XTandem Parser lists: ProteoWizard lists: Maltcms lists: multiplierz lists: ADTEx lists: MatNMR lists: GSim lists: RASP lists: TE-locate lists: FIGG lists: Bpredictor lists: DIYA lists: MrBayes lists: Fastphylo lists: PhyloTreePruner lists: SNP ratio test lists: MOABS lists: CAMPways lists: compomics-utilities lists: DeNovoGUI lists: ProteoCloud lists: kruX lists: FingerID lists: proTRAC lists: SlideSort-BPR lists: SPINAL lists: HopeMap lists: SketchEl lists: GLARE lists: MCDL lists: NetMODE lists: Toxtree lists: Toxmatch lists: Viewmol lists: QuteMol lists: AHA lists: PBJelly lists: SAM format lists: PSimScan lists: NetCoffee lists: COBRApy lists: ORCA lists: Bionotate lists: Knowtator lists: MMAX2 lists: LAITOR lists: Connecting Overlapped Pair-End reads lists: iPapers lists: PyPedal lists: miRPlant lists: Simulate PCR lists: Scalpel lists: SAT-Assembler lists: CONDEX lists: ChiBE lists: diCal-IBD lists: MToolBox lists: ReviSTER lists: Allim lists: Ionwinze lists: VirVarSeq lists: GeneVenn lists: Pegasus-fus lists: GenoSIGHT lists: Cell motility lists: MSImageViewer lists: GlycReSoft lists: GlycanBuilder lists: ISDTool lists: cnvCapSeq lists: EC2KEGG lists: npstat lists: PoolHap lists: eALPS lists: LDx lists: PLEK lists: REDItools lists: NAIL lists: iMSAT lists: PrimerProspector lists: iceLogo lists: NESmapper lists: DHAC lists: AMS lists: Musite lists: PhosphoSiteAnalyzer lists: xMSanalyzer lists: MP-EST lists: HLAforest lists: LocalAli lists: A5-miseq lists: WaveCNV lists: Burrows-Wheeler transform lists: DNAcopy lists: CRLMM lists: motifRG lists: CNV Workshop lists: MotifLab lists: MMDiff lists: MiRaGE lists: OncoSNP-SEQ lists: LVSmiRNA lists: ExiMiR lists: OpenHelix Blog lists: EXCAVATOR-tool lists: RPA lists: CexoR lists: SWIPE lists: Isaac lists: CRAVAT lists: CMA lists: lumi lists: baySeq lists: edgeR lists: tRanslatome lists: SIFT lists: DNaseR lists: ANNOVAR lists: DEXSeq lists: ChIPpeakAnno lists: inSilicoMerging lists: minfi lists: Methylumi lists: miRNApath lists: affy lists: sva package lists: ArrayTrack lists: NGSmethDB lists: dmrFinder lists: Amazon Web Services lists: BEDOPS lists: rqubic lists: R-Bloggers.com lists: BicARE lists: iBBiG lists: eisa lists: Trowel lists: ChAMP lists: Acacia lists: cghMCR lists: GEN lists: Ngs backbone lists: Blue Collar Bioinformatics lists: Bioconductor mailing list lists: NCBI Assembly Archive Viewer lists: DiffBind lists: featureCounts lists: NarrowPeaks lists: GeneProf lists: DROMPA lists: CSAR lists: CSSP lists: TargetScore lists: CAZy lists: U.S. Food and Drug Administration lists: snapCGH lists: PhyloTree.org lists: MitoBreak lists: iChip lists: miRDeep* lists: CloudAligner lists: TurboNorm lists: InCroMAP lists: ProbeSelect lists: OligoWiz lists: GenomeView lists: SeqGenome Browser lists: GBrowse syn lists: MIG lists: Ringo lists: CRAM lists: Centers for Disease Control and Prevention lists: KungFq lists: SAMZIP lists: EDNA lists: MSAProbs lists: RLMM lists: OncoSNP lists: Onco-STS lists: ChIPOTle Peak Finder lists: charm lists: BiSeq lists: NxGview lists: MEDME lists: MEDIPS lists: MethylCoder lists: BSmapper lists: GRASSIUS lists: QcReads lists: SeqPrep lists: HECTOR lists: SHREC lists: hiCtools lists: BayesPeak lists: FishMicrosat lists: ChIPseqR lists: Rolexa lists: Swift lists: TraceTuner lists: seqMINER lists: miRecords lists: ComiR lists: MIReNA lists: MIREAP lists: miRDeep-P lists: RSEM lists: ncPRO-seq lists: AUTO-MUTE lists: vcf2MSAT lists: TopHat lists: cn.mops lists: SAMMate lists: FishingCNV lists: ABACUS lists: NGSpeAnalysis lists: Bamformatics lists: Genotype-Tissue Expression lists: IBDLD lists: HATS lists: SolSNP lists: RankProd lists: Trinity lists: Multivariate Analysis of Transcript Splicing lists: SNVMix lists: SNPTools lists: MendelScan lists: LoFreq lists: IMPUTE2 lists: GENE-counter lists: RNA CoMPASS lists: CoNAn-SNV lists: VCAKE lists: PRICE lists: LOCAS lists: Edena v3 lists: Contrail lists: AMOS lists: A5 lists: VDJFasta lists: Reptile lists: phyloseq lists: PhyloPhlAn lists: RDP FrameBot lists: QuantiSNP lists: Celera Genome Browser lists: AutoMap lists: mGOASVM lists: Genetic Genealogist lists: DSP lists: BRAT lists: cnvHiTSeq lists: Easyfig lists: ENA Sequence Search lists: bisReadMapper lists: palfinder lists: HiTC lists: IsoLasso lists: sam comp lists: CancerMutationAnalysis lists: muliAlignFree lists: CongrPE lists: CallSim lists: Tuxedo lists: SAPAS lists: PolyPhen-2 lists: GoGrid lists: Telescoper lists: RegRNA lists: dbCAN lists: HeurAA lists: CoNIFER lists: DiffSplice lists: MAP lists: DynamicProg lists: NGS Expert Blog lists: genCAT lists: SOCS lists: Monoclonal Antibody Index lists: BEADS lists: aCGH lists: RepeatSeq lists: CEM lists: Repitools lists: SeqSite lists: SmashCommunity lists: eProbalign lists: GPSeq lists: Antibody Links lists: SOAPsplice lists: CEDER lists: miRSeqNovel lists: PIA lists: SOAPdenovo-Trans lists: Wgsim lists: ChimeraSlayer lists: Mpstruct lists: RDXplorer lists: wapRNA lists: SeqTRACS lists: chimerascan lists: Human Transcriptome Database for Alternative Splicing lists: Crossbow lists: Cufflinks lists: HMMSplicer lists: MicroRazerS lists: psRNATarget lists: Trans-ABySS lists: NEUMA lists: Homologus lists: FusionSeq lists: Probalign lists: PLAN2L lists: DSAP lists: MEDEA lists: CNV-seq lists: GENSCAN lists: Alta-Cyclic lists: RosettaDock lists: MethyCancer lists: MED lists: PLACE- A Database of Plant Cis-acting Regulatory DNA Elements lists: Drosophila melanogaster Exon Database lists: RARTF lists: INCLUSive lists: ArrayOligoSelector lists: TreeView lists: dChip Software lists: Cluster lists: dChip Software lists: ScanAlyze lists: Avadis lists: GONUTS lists: PiNGO lists: KLEIO lists: ClinicalTrials.gov lists: Gene Ontology lists: Neuroscience Information Framework lists: ArrayExpress lists: SGD lists: SEQanswers Wiki lists: SMD lists: GOSlimViewer lists: OntoVisT lists: STRAP lists: GoFish lists: GOProfiler lists: FuncAssociate: The Gene Set Functionator lists: UCSC Genome Browser lists: UniPROBE lists: GREAT: Genomic Regions Enrichment of Annotations Tool lists: Whatizit lists: REViGO lists: Blast2GO lists: InterProScan lists: DiseaseMeth lists: caArray lists: NCBI Epigenomics lists: OMIM lists: Mouse Genome Informatics (MGI) lists: European Nucleotide Archive (ENA) lists: FlyBase lists: Ontology Lookup Service lists: MaizeGDB lists: Dictyostelium discoideum genome database lists: InterPro lists: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit lists: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool lists: RamiGO lists: GeneCodis lists: IntAct lists: agriGO lists: GOblet lists: Gene Expression Omnibus lists: Biological General Repository for Interaction Datasets (BioGRID) lists: Ingenuity Pathway Analysis lists: Roadmap Epigenomics Project lists: PEER lists: KEGG lists: Antibodypedia lists: AcroMine lists: g:Profiler lists: HighWire Press lists: Biometric Research Branch: ArrayTools lists: R Project for Statistical Computing lists: Nu-OSCAR lists: Pedigree-Draw lists: Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis lists: ChIP-Atlas lists: ProLinks Database of Functional Linkages lists: Myrna lists: lilikoi lists: GOTrack lists: Ximmer lists: NAT/NCS2 Hound lists: VoxBlast lists: Splicing Express lists: RNA22 lists: miRWalk lists: miRmap lists: AbundantOTU+ lists: MutaGene lists: VecScreen lists: NMRProcFlow lists: Attie Lab Diabetes Database lists: Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS lists: XYalign lists: fermi lists: metaPocket lists: DoG picker lists: TiltPicker lists: NeuroAnatomy Toolbox lists: MAxEntScan lists: MetaNeighbor lists: OmicsNet lists: Discovar assembler lists: Supernova assembler lists: Epik lists: Ligprep lists: PathwayMatcher lists: EMAN lists: Geno2MP lists: duphold lists: ConsensusClusterPlus lists: EpiFactors lists: fastp lists: NanoFilt lists: Heatmapper lists: Nuclear Hormone Receptor Scan lists: Metacell lists: OmicsSIMLA lists: ScaffMatch lists: MITE-Tracker lists: PCAGO lists: BinPacker lists: Bridger lists: RaceID lists: PRSice lists: cwl-metrics lists: mzStudio lists: OrthoFinder lists: SwiftOrtho lists: ClustVis lists: CWL-Airflow lists: CytExpert Software lists: Computational Suite for Bioinformaticians and Biologists lists: WTDBG lists: prank lists: MACS lists: NeuroAnatomy Toolbox lists: CentroidFold lists: pKiss lists: BIDS Validator lists: PILER lists: trimAl lists: NOVOPlasty lists: GeSeq lists: Diffusion Toolkit lists: PathwayNet lists: miRTarBase lists: CLC Genomics Workbench lists: PyNWB lists: FastProject lists: DiseaseMeth lists: WormAtlas lists: GeneATLAS lists: immuneXpresso lists: BioAssay Express lists: ChemRICH lists: TransDecoder lists: GADMA lists: Alien-hunter lists: ALTER lists: AMAP lists: Anfo lists: Aragorn lists: Arden lists: Ariba lists: Augustus lists: Avogadro lists: Axe lists: Baitfisher lists: BALLView lists: Bamtools lists: Barrnap lists: BEAST lists: BioPerl lists: bioSyntax lists: Bio-tradis lists: BOXSHADE 3.21 lists: Canu lists: Cassiopee lists: Cdbfasta lists: CD-HIT lists: Circlator lists: Clearcut lists: Clonalframe lists: ClonalOrigin lists: Clustal W2 lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: Concavity lists: Cufflinks lists: cwltool lists: DIAMOND lists: DISULFIND lists: Database of Secondary Structure Assignments lists: Eigensoft lists: EMBOSS lists: ESTScan lists: FASTLINK lists: FastQC lists: FastTree lists: FigTree lists: Fsm-lite lists: Gamgi lists: Genome BioInformatics Research Lab - gff2ps lists: Ghemical lists: GIIRA lists: GROMACS lists: Gwyddion lists: Bioinformatics Toolkit lists: PyMOL lists: Biopython lists: PRESTO: Genetic Association Analysis Software lists: CummeRbund lists: ProtTest lists: Prokka lists: Computational Structural Biology Toolbox lists: LEfSe lists: jModelTest lists: khmer lists: Atac lists: LAMARC lists: FreeContact lists: libRoadRunner lists: TFBS lists: MicrobiomeUtilities lists: MINIMAC lists: MultiQC lists: Nanopolish lists: IgBLAST lists: PHYLIP lists: PhyML lists: Pilon lists: ADEGENET lists: phytools lists: R/QTL lists: RDKit: Open-Source Cheminformatics Software lists: RepeatMasker lists: SeaView lists: SEER lists: Seq-Gen lists: StringTie lists: THESIAS lists: Transterm lists: Vascular Modeling Toolkit lists: Aegean lists: andi lists: Bandage lists: Eagle lists: BioJava Project lists: Bio++ lists: BRAKER lists: Bustools lists: Centrifuge Classifier lists: ChromHMM lists: DeepNano lists: Ecopcr lists: Edtsurf lists: E-mem lists: Examl lists: Falcon lists: Fastaq lists: Fastml lists: Fastqtl lists: FSA lists: GARLI lists: Garlic lists: gdpc lists: GenomeTools lists: Gentle lists: Gff2aplot lists: gffread lists: GraPhlAn lists: Gubbins lists: Harvest-tools lists: HiLive lists: Hinge lists: HyPhy lists: Indelible lists: IQ TREE lists: Fastahack lists: Mash lists: MEGAHIT lists: Minimap2 lists: mosdepth lists: MUMmer lists: OptiType lists: Phyutility lists: Porechop lists: QIIME2 lists: Racon lists: Phangorn lists: pheatmap lists: Recognition of Errors in Assemblies using Paired Reads lists: RELION lists: Roary lists: Salmon lists: Scoary lists: University of Zurich SCRM - Cell-and Tissue Biobank lists: Seqtk lists: Short Read Sequence Typing for Bacterial Pathogens lists: Vmatch lists: ABACAS lists: AceDB lists: tRNAscan-SE lists: Antibody Resource Page is related to: COnsensus-DEgenerate Hybride Oligonucleotide Primers is related to: Classifier for Metagenomic Sequences is related to: Pedigree-Draw is related to: CAZy- Carbohydrate Active Enzyme is related to: PolyPhen: Polymorphism Phenotyping is related to: BioRAT is related to: dChip Software is related to: Rat Genome Database (RGD) is related to: Comparative Toxicogenomics Database (CTD) is related to: VISTA Enhancer Browser is related to: affy |
PMID:25024350 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155571, r3d100012426 | https://doi.org/10.17616/R3PJ3N | http://omictools.com/ | SCR_002250 | SciCrunch Registry | genOMIC tools | 2026-10-31 12:13:03 | 34 | ||||
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Babelomics Resource Report Resource Website 100+ mentions |
Babelomics (RRID:SCR_002969) | Babelomics | analysis service resource, data analysis service, production service resource, service resource | An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system . Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements: * Data input: import and quality control for the most common microarray formats * Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent). * Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis. * Genotyping: stratification analysis, association, TDT. * Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis. * Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis. Platform: Online tool | platform, analysis, transcriptomics, proteomics, genomics, normalization, clustering, gene, mirna, protein, interaction, text mining, genotyping, bioentity, functional profiling, statistical analysis, functional annotation, regulatory motif, microarray, fatigo, biclustering, networkminer, gepas, gene expression, FASEB list |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG is related to: TRANSFAC is related to: JASPAR has parent organization: CIPF Bioinformatics and Genomics Department |
Spanish Ministry of Science and Innovation BIO2008-04212; Spanish Ministry of Science and Innovation CEN-2008-1002; Red Temtica de Investigacion Cooperativa en Cancer RD06/0020/1019; Instituto de Salud Carlos III |
PMID:20478823 PMID:18515841 PMID:16845052 PMID:14990455 PMID:15980512 PMID:17478504 |
Free for academic use, Account required | OMICS_00748, nif-0000-30144 | http://www.fatigo.org/, http://www.gepas.org/, http://babelomics3.bioinfo.cipf.es | http://www.babelomics.org | SCR_002969 | SciCrunch Registry | Babelomics 4: Gene Expression and Functional Profiling Analysis Suite, Babelomics 4 | 2026-10-31 12:19:55 | 138 | |||
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NCBI BioSystems Database Resource Report Resource Website 100+ mentions |
NCBI BioSystems Database (RRID:SCR_004690) | BioSystems | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them. | pathway, disease, gene, protein, small molecule, literature, computation, image, biomarker, drug, structural complex, functional set, biological system, molecule, gold standard, bio.tools |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: KEGG is related to: NCBI Structure is related to: BioCyc is related to: EcoCyc is related to: MetaCyc is related to: Reactome is related to: Pathway Interaction Database is related to: WikiPathways is related to: Gene Ontology has parent organization: NCBI |
NIH | PMID:19854944 | r3d100011033, biotools:biosystems, nlx_69646 | https://bio.tools/biosystems, https://doi.org/10.17616/R31K80 | SCR_004690 | SciCrunch Registry | BioSystems Database, NCBI BioSystems | 2026-10-31 12:13:54 | 118 | |||||
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NIF Data Federation Resource Report Resource Website 10+ mentions |
NIF Data Federation (RRID:SCR_004834) | Data Federation | data or information resource, portal, service resource | Service that partners with the community to expose and simultaneously drill down into individual databases and data sets and return relevant content. This type of content, part of the so called hidden Web, is typically not indexed by existing web search engines. Every record links back to the originating site. In order for NIF to directly query these independently maintained databases and datasets, database providers must register their database or dataset with the NIF Data Federation and specify permissions. Databases are concept mapped for ease of sharing and to allow better understanding of the results. Learn more about registering your resource, http://neuinfo.org/nif_components/disco/interoperation.shtm Search results are displayed under the Data Federation tab and are categorized by data type and nervous system level. In this way, users can easily step through the content of multiple resources, all from the same interface. Each federated resource individually displays their query results with links back to the relevant datasets within the host resource. This allows users to take advantage of additional views on the data and tools that are available through the host database. The NIF site provides tutorials for each resource, indicated by the Professor Icon professor icon showing users how to navigate the results page once directed there through the NIF. Additionally, query results may be exported as an Excel document. Note: NIF is not responsible for the availability or content of these external sites, nor does NIF endorse, warrant or guarantee the products, services or information described or offered at these external sites. Integrated Databases: Theses virtual databases created by NIF and other partners combine related data indexed from multiple databases and combine them into one view for easier browsing. * Integrated Animal View * Integrated Brain Gene Expression View * Integrated Disease View * Integrated Nervous System Connectivity View * Integrated Podcasts View * Integrated Software View * Integrated Video View * Integrated Jobs * Integrated Blogs For a listing of the Federated Databases see, http://neuinfo.org/mynif/databaseList.php or refer to the Resources Listed by NIF Data Federation table below. | semantics, neuroscience, animal, annotation, antibody, biospecimen, brain activation foci, clinical trial, connectivity, dataset, disease, drug, grant, image, microarray, model, multimedia, negative data, pathway, people, plasmid, registry, software, brain region, cell, gene, molecule, multi-level, nervous system, nervous system function, model |
uses: MNI Podcasts uses: Educational Resources in Neuroscience uses: Mind Hacks uses: BAMS Nested Regions uses: Indeed uses: NINDS Disorder Index uses: Drug Design Data Resource uses: PubMed Health uses: This Week In Science uses: Science Talk uses: BAMS Connectivity uses: Lady Scientist uses: Psychology Corner uses: Wired Science uses: CENtral Science uses: RetractionWatch.com uses: The Guardian: Science Weekly uses: H2SO4Hurts uses: 60-Second Mind uses: PLoS Blogs uses: Clarity resources uses: Open Source Brain uses: Diabetic Complications Consortium uses: Integrated Animals uses: Kawasaki Disease Dataset uses: EEGbase uses: Integrated Models uses: Lifespan Observations Database uses: NIF Web Services uses: NIF Blog uses: ATCC uses: Cerebellar Platform uses: Brain Machine Interface Platform uses: Rafael Yustes Laboratory uses: ASAP uses: NIH VideoCasting uses: NIDA Data Share uses: Neurofed uses: Candida Genome Database uses: Addgene uses: ASPGD uses: Glomerular Activity Response Archive uses: WikiPathways uses: AmiGO uses: NeuroMorpho.Org uses: Cell Centered Database uses: Integrated uses: Community Structure-Activity Resource uses: ClinicalTrials.gov uses: Ensembl uses: GeneNetwork uses: Avian Brain Circuitry Database uses: EcoCyc uses: Entrez Gene uses: Zebrafish Information Network (ZFIN) uses: Arredondo ANT fNIRS dataset1 uses: Grants.gov uses: T3DB uses: Simtk.org uses: PharmGKB uses: DrugBank uses: Aging Genes and Interventions Database uses: Gene Expression Nervous System Atlas uses: SumsDB uses: bioDBcore uses: BioNumbers uses: Gene Ontology uses: Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat uses: Gramene uses: Retina Project uses: HomoloGene uses: ArrayExpress uses: Journal of Visualized Experiments uses: Allen Mouse Brain Reference Atlas uses: Gene Weaver uses: Visiome Platform uses: Developmental Therapeutics Program uses: NeuroMab uses: WormBase uses: NeuronDB uses: Integrated Grants uses: studyforrest.org uses: BrainInfo uses: Mouse Phenome Database (MPD) uses: NCBI Taxonomy uses: NCBI Protein Database uses: Psychoactive Drug Screening Program Ki Database uses: Nuclear Receptor Signaling Atlas uses: Brede Database uses: NeuroImaging Tools and Resources Collaboratory (NITRC) uses: Mouse Genome Informatics Transgenes uses: Reactome uses: Cell Image Library (CIL) uses: BAMS Cells uses: Synapse Web uses: Integrated Videos uses: NeuroVault uses: Royal College of Psychiatrists Podcasts uses: WU-Minn HCP 500 Subjects MR and MEG Release uses: Data.gov Science and Research Data Catalog uses: NITRC-IR uses: One Mind Biospecimen Bank Listing uses: Integrated Brain Gene Expression uses: BrainSpan uses: All In The Mind uses: Scientific American Cross-Check uses: PubChem uses: NeuroPod uses: BrainSpan uses: Health.Data.gov uses: Biointeractive uses: UniProtKB uses: Gray Matters uses: dkCOIN uses: Brain Science Podcast uses: NIGMS Human Genetic Cell Repository uses: DISCO uses: GeneDB Lmajor uses: TAIR uses: ScienceNOW uses: Daily Scan uses: SGD uses: Integrated Software uses: BrainPod uses: GeneDB Tbrucei uses: MPO uses: PANTHER uses: Neurology Podcast uses: Integrated Disease uses: VMD uses: UCSF Laboratory for Visual Neuroscience uses: NIMH Chemical Synthesis and Drug Supply Program uses: NIH Neuroscience Microarray Consortium uses: SGN uses: Protocol Online - Your labs reference book uses: Integrated Podcasts uses: OpenNeuro uses: National Academy of Sciences Podcasts uses: Beta Cell Biology Consortium uses: Naturejobs uses: Scientific American Guest Blog uses: jobs.ac.uk uses: New Scientist Jobs uses: Science Careers uses: Access-ScienceJobs.co.uk uses: ScienceBlogs: Life Science uses: ScienceBlogs: Brain and Behavior uses: TheScienceJobs.com uses: Nature Network Blogs uses: The Guardian: Science uses: LabSpaces uses: ScienceBlogs: Medicine and Health uses: Scientific American Observations uses: Scientific American Bering in Mind uses: QUEST uses: Daring Nucleic Adventures - genegeek uses: Oxford Science Blog uses: Sciblogs uses: New York Times - Well uses: SciLogs uses: Cassandras Tears uses: BioPortfolio uses: Now at NEJM uses: 1000 Functional Connectomes Project uses: Integrated Jobs uses: Integrated Blogs uses: JCVI CMR uses: SciCrunch Registry uses: Neuroskeptic uses: CRCNS uses: Expression Atlas of the Marmoset uses: IXI dataset uses: Integrated Auto-Extracted Annotation uses: EU Clinical Trials Register uses: Integrated Clinical Trials uses: Human Brain Atlas uses: goCognitive uses: Law and Neuroscience uses: International Mouse Phenotyping Consortium (IMPC) uses: ClinVar uses: Integrated Gene-Disease Interaction uses: XNAT Central uses: neuroelectro uses: Integrated Nervous System Connectivity uses: Antibody Registry uses: OMIA - Online Mendelian Inheritance in Animals uses: OMIM uses: Science Podcast uses: Mouse Genome Informatics (MGI) uses: Monster uses: NCBI uses: Wired Science Blogs uses: F1000 Posters uses: Neurophilosophy uses: Comparative Toxicogenomics Database (CTD) uses: FlyBase uses: GeneReviews uses: GeneDB Pfalciparum uses: Naturally Selected uses: PomBase uses: Pseudomonas Genome Database uses: The Guardian: Science Videos uses: Orphanet uses: Dictyostelium discoideum genome database uses: PeptideAtlas uses: NeuroSynth uses: neuropathology blog uses: Genomes Unzipped uses: National Institutes of Health Research Portfolio Online Reporting Tool uses: BrainMaps.org uses: It Takes 30 uses: Gait in Parkinson's Disease uses: Physiobank uses: Gait Dynamics in Neuro-Degenerative Disease Data Base uses: American Journal of Psychiatry Podcasts uses: Neurodatabase.org uses: Brain Architecture Management System uses: RanchoBiosciences uses: ModelDB uses: CoCoMac uses: Olfactory Bulb Odor Map DataBase (OdorMapDB) uses: Gene Expression Omnibus uses: Caenorhabditis Genetics Center uses: Labome uses: Open Access Series of Imaging Studies uses: Biological General Repository for Interaction Datasets (BioGRID) uses: Olfactory Receptor DataBase uses: T1DBase uses: Gemma uses: CellML Model Repository uses: ResearchCrossroads uses: Biocompare uses: BioNOT uses: Hays uses: Research Blogging uses: Discover Magazine uses: PolygenicBlog uses: Kawasaki Disease Dataset2 uses: Allen Mouse Brain Connectivity Atlas uses: Integrated Manually Extracted Annotation uses: Roadmap Epigenomics Project uses: Integrated Cell Lines uses: National Mouse Metabolic Phenotyping Centers uses: Mendelspod uses: Integrated Snippets uses: Integrated Datasets uses: Nature Podcast uses: GWAS: Catalog of Published Genome-Wide Association Studies uses: KEGG uses: USC Multimodal Connectivity Database uses: Inside NIA: A Blog for Researchers uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: NIF Registry Automated Crawl Data uses: Genetic Analysis Software uses: anage uses: Intestinal Stem Cell Consortium uses: Animal QTLdb uses: elements of morphology uses: Human Life-Table Database uses: Clinical Genomic Database uses: NIDDK Central Repository uses: MONARCH Initiative uses: Human Phenotype Ontology is used by: SciCrunch is used by: NIDDK Information Network (dkNET) lists: AutDB lists: Drug Related Gene Database lists: Gene Ontology Tools lists: CHEBI is listed by: 3DVC is related to: International Mouse Strain Resource is related to: Internet Brain Volume Database is related to: Resource Identification Portal is related to: Rat Genome Database (RGD) is related to: VISTA Enhancer Browser is related to: NIH Human Pluripotent Stem Cell Registry is related to: Zebrafish International Resource Center is related to: Bloomington Drosophila Stock Center is related to: Journal of Comparative Neurology Antibody database has parent organization: Neuroscience Information Framework |
NIDA ; NIH Blueprint for Neuroscience Research ; U.S. Department of Health and Human Services HHSN27120080035C |
Refer to individual databases | nlx_81822 | http://neuinfo.org/nif/nifgwt.html?query=* | SCR_004834 | SciCrunch Registry | Neuroscience Information Framework Data Federation | 2026-10-31 12:19:09 | 28 | |||||
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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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