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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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Iowa State University Genome Informatics Core Facility Resource Report Resource Website |
Iowa State University Genome Informatics Core Facility (RRID:SCR_017790) | GIF | access service resource, core facility, service resource | Provides help with grant review, information on data management plans,suggestion best practices for bionformatics analyses, advise on experimental design for Next Gen Sequencing (NGS) projects.Services include:Genome assembly and annotation,Transcriptome assembly and annotation,SNP/InDel calling,RNA-Seq analysis,ChiP-seq,Introgression mapping,novel gene discovery,Personalized GBrowse instances for data visualization,Access to high performance computing, Custom big data projects. | Genome, informatics, data, management, analysis, design, grant, service, core | Open | ABRF_422 | SCR_017790 | Genome Informatics Facility | 2026-08-04 09:44:17 | 0 | ||||||||
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CHARMM Resource Report Resource Website 500+ mentions |
CHARMM (RRID:SCR_014892) | simulation software, software application, software resource | Software program that simulates molecular interactions. It has features that allow broad application to many-particle systems with a comprehensive set of energy functions, a variety of enhanced sampling methods, and support for multi-scale techniques, and a range of implicit solvent models. It also primarily targets biological systems including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. CHARMM can also be applied to inorganic materials with applications in materials design and has a comprehensive set of analysis and model builiding tools. | visualization, modeling, molecular simulation, materials design, model building tools, analysis, biological systems, peptides, proteins | is used by: CHARMM-GUI | SCR_014892 | 2026-08-04 09:43:32 | 936 | |||||||||||
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FLIMfit Resource Report Resource Website 1+ mentions |
FLIMfit (RRID:SCR_016298) | software application, software resource, software toolkit | Software package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | fluorescence, lifetime, imaging, microscopy, dataset, global, analysis, multiwell, plate, routine | United Kingdom Biotechnology and Biological Sciences Research Council BBSRC BB/E003621/1; United Kingdom Technology Strategy Board Technology Award CHBT/007/00030; Wellcome Trust WT 095931/Z/11/Z |
PMID:23940626 DOI:10.1371/journal.pone.0070687 |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/flimfit/FLIMfit | SCR_016298 | 2026-08-04 09:43:52 | 3 | ||||||||
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VisIt Resource Report Resource Website |
VisIt (RRID:SCR_024370) | software application, software resource | Open source software interactive, scalable, visualization, animation and analysis tool. Used to generate visualizations, animate them through time, manipulate them with variety of operators and mathematical expressions, and save resulting images and animations for presentations. | generate visualizations, animation, analysis, save resulting images and animations for presentations, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/visit/ | SCR_024370 | visit | 2026-08-04 09:45:31 | 0 | ||||||||
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National Magnetic Resonance Facility at Madison Resource Report Resource Website 1+ mentions |
National Magnetic Resonance Facility at Madison (RRID:SCR_001449) | NMRFAM | access service resource, training resource, service resource | Provides access and developes NMR technology to advance range of applications and improves the efficiency, rigor and reproducibility of NMR data acquisition and analysis. Houses NMR spectrometers equipped with state-of-the-art probe technology and protocols to support acquisition of high-quality data. Spectrometers range from 500 MHz to 1100 MHz. Service is tailored to the needs of individual users and projects. Provides training and advice on experimental design, best practices for data acquisition, and data analysis. Experienced staff support users with training opportunities including workshops, video tutorials and protocols. | nmr spectrometer, structure, function, protein, rna, dynamics, complex, membrane protein, paramagnetic protein, metabolomics, analysis, spectroscopy, nucleic acid, automation, data analysis, macromolecule, small angle x-ray scattering, structural biology technology center | has parent organization: University of Wisconsin-Madison; Wisconsin; USA | NIGMS R24GM141526; NIGMS P41136463 |
Free, Freely Available | nlx_152672 | SCR_001449 | 2026-08-04 09:40:23 | 4 | |||||||
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Hunter Genomic Facility Resource Report Resource Website |
Hunter Genomic Facility (RRID:SCR_001983) | access service resource, core facility, service resource | Facility which provides instruments and instrument resources for analyzing DNA, RNA, protein, and radio-labeled substances. | genomics, dna, rna, protein, analysis, core facility |
is listed by: Eagle I has parent organization: Hunter College; New York; USA |
Instruction required, Fee | nlx_156341 | http://hunter-cuny.eagle-i.net/i/00000136-7e34-9f73-949b-425080000000 | SCR_001983 | 2026-08-04 09:40:31 | 0 | ||||||||
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National Resource for Network Biology Resource Report Resource Website 1+ mentions |
National Resource for Network Biology (RRID:SCR_004259) | NRNB | biomedical technology research center, training resource | Biomedical technology research center that develops new algorithms, visualizations and conceptual frameworks to study biological networks at multiple levels and scales, from protein-protein and genetic interactions to cell-cell communication and vast social networks. They are developing freely available, open-source suite of software technology that broadly enables network-based visualization, analysis, and biomedical discovery for NIH-funded researchers. This software is enabling researchers to assemble large-scale biological data into models of networks and pathways and to use these networks to better understand how biological systems operate under normal conditions and how they fail in disease. The National Resource for Network Biology is organized around the following key components: Technology Research and Development, Driving Biomedical Projects, Outreach, Training and Dissemination of Tools. The NRNB supports several types of training events, including both virtual and live workshops; tutorials sessions for clinicians, biologists and bioinformaticians; presentations and demonstrations at conferences; online tutorials and webcasts; and annual symposium. | protein-protein interaction, interaction, cell, cell communication, network, model, pathway, biological system, disease, visualization, analysis, biomedical, computing and informatics technology center | has parent organization: University of California at San Diego; California; USA | NIGMS GM103504; NCRR RR031228 |
nlx_27231 | SCR_004259 | 2026-08-04 09:41:06 | 6 | ||||||||
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NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis Resource Report Resource Website 1+ mentions |
NIH / NCRR Mass Spectrometry Resource Washington University in St. Louis (RRID:SCR_009009) | Mass Spectrometry Resource, WU Mass Spectrometry Resource | biomedical technology research center, training resource | Biomedical technology research center that develops mass spectrometry-based tools for the study of proteins, lipids and metaboilites. These include biomarker identification, stable isotope mass spectrometry and the analysis of intact proteins. Our goals are: * to conduct basic research in the science of mass spectrometry * to establish collaborative research projects with scientists at WU and at other institutions * to provide a service in mass spectrometry * to educate and train students in mass spectrometry * to disseminate results of our research and descriptions of the subject of mass spectrometry | systems biology technology center, mass spectrometry, protein, lipid, metaboilite, biomarker, isotope, analysis | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIGMS ; NCRR 2P41RR00954 |
nlx_152688 | SCR_009009 | Mass Spectrometry Resource at Washington University in St. Louis, Washington University Mass Spectrometry Resource | 2026-08-04 09:42:17 | 1 | |||||||
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Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center Resource Report Resource Website |
Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center (RRID:SCR_009668) | BIDMC Genomics, Proteomics, Bioinformatics and Systems Biology Center | access service resource, core facility, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core provides services: RT PCR service, Gene expression profiling service, Proteomics analysis service, Bioinformatics and Systems Biology analyses, Next Generation Sequencing Service, Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates. Core proteomics facility for the Dana-Farber/Harvard Cancer Center. Workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq, Comprehensive workflow for analysis of Microbiome sequencing data, Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data. Pipelines: MALDI Tissue imaging and targeted quantitative proteomics. | RT PCR, transcriptome, epigenome, metabolomics, profiling, assay, protein, expression, pathway, data, bioinformatics, analysis, next, generation, sequencing, human, mouse, array, tissue, imaging |
is listed by: Eagle I is related to: Beth Israel Deaconess Medical Center Labs and Facilities is related to: Harvard University Labs and Facilities has parent organization: Harvard University; Cambridge; Massachusetts |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156126 | http://www.bidmcgenomics.org/ | SCR_009668 | Beth Israel Deaconess Medical Center, BIDMC | 2026-08-04 09:42:27 | 0 | ||||||
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Dana-Farber Cancer Institute Molecular Biology Core Facility Resource Report Resource Website 1+ mentions |
Dana-Farber Cancer Institute Molecular Biology Core Facility (RRID:SCR_009754) | MBCF at DFCI | access service resource, core facility, service resource | Core offers services for genomic next-generation sequencing library preparation, sequencing and analysis applications including RNAseq, ChIPseq, ATACseq, CRISPR screening, whole genome methylation profiling, targeted resequencing, single-cell RNAseq, exome sequencing, and more. Performs bioinformatics analysis such as integration of multi-omics datasets or specialized analyses. Genomics core technology platforms include Illumina NovaSeq6000, NextSeq500s, MiSeqs, MiniSeq. High throughput sample preparation is performed on Beckman Coulter Biomek FX and i7 systems. Low throughput samples are prepared by technical staff. | Next generation sequencing, RNAseq, ChIPseq, ATACseq, CRISPR, analysis, dataset, genomics, ABRF |
is listed by: Eagle I is listed by: ABRF CoreMarketplace has parent organization: Dana-Farber Cancer Institute |
Open | nlx_156214, SCR_018264, ABRF_57 | https://coremarketplace.org/?FacilityID=57 | http://harvard.eagle-i.net/i/0000012a-2512-3484-5617-794280000000 | SCR_009754 | , Dana-Farber Cancer Institute Molecular Biology Core Facilities, DFCI Molecular Biology Core Facilities | 2026-08-04 09:42:27 | 1 | |||||
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Kidney Tissue Atlas Resource Report Resource Website 10+ mentions |
Kidney Tissue Atlas (RRID:SCR_021626) | atlas, data or information resource | Atlas is set of interactive tools built to promote retrieval, exploration, discovery, and analysis of Kidney Precision Medicine Project data by greater research community. Datasets available in repository are combination of raw and processed data from KPMP participant biopsies and reference tissue samples. | Interactive tools, retrieval, exploration, discovery, analysis, Kidney Precision Medicine Project data | is related to: Kidney Precision Medicine Project | Free, Freely available | SCR_021626 | 2026-08-04 09:44:51 | 23 | ||||||||||
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TARGETgene Resource Report Resource Website 1+ mentions |
TARGETgene (RRID:SCR_001392) | TARGETgene | software application, software resource | MATLAB tool to effectively identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. It can rapidly extract genetic interactions from a precompiled database stored as a MATLAB MAT-file without the need to interrogate remote SQL databases. Millions of interactions involving thousands of candidate genes can be mapped to the genetic network within minutes. While TARGETgene is currently based on the gene network reported in (Wu et al.,Bioinformatics 26:807-813, 2010), it can be easily extended to allow the optional use of other developed gene networks. The simple graphical user interface also enables rapid, intuitive mapping and analysis of therapeutic targets at the systems level. By mapping predictions to drug-target information, TARGETgene may be used as an initial drug screening tool that identifies compounds for further evaluation. In addition, TARGETgene is expected to be applicable to identify potential therapeutic targets for any type or subtype of cancers, even those rare cancers that are not genetically recognized. Identification of Potential Therapeutic Targets * Prioritize potential therapeutic targets from thousands of candidate genes generated from high-throughput experiments using network-based metrics * Validate predictions (prioritization) using user-defined benchmark genes and curated cancer genes * Explore biologic information of selected targets through external databases (e.g., NCBI Entrez Gene) and gene function enrichment analysis Initial Drug Screening * Identify for further evaluation existing drugs and compounds that may act on the potential therapeutic targets identified by TARGETgene * Explore general information on identified drugs of interest through several external links Operating System: Windows XP / Vista / 7 | disease target, drug discovery, drug, matlab, gene network, genetic interaction, gene, drug screening, mutation driver, therapeutic target, drug candidate, compound, mapping, analysis | has parent organization: Biomedical Simulations Resource | Cancer | NIBIB P41-EB001978 | PMID:22952662 | Free, Under the terms of a Release Agreement., Please cite | nlx_152573 | http://bmsr.usc.edu/Software/TARGET/TARGET.html | SCR_001392 | 2026-08-04 09:40:22 | 7 | ||||
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Blast2GO Resource Report Resource Website 5000+ mentions |
Blast2GO (RRID:SCR_005828) | B2G | software application, software resource | An ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data. Blast2GO (B2G) joins in one universal application similarity search based GO annotation and functional analysis. B2G offers the possibility of direct statistical analysis on gene function information and visualization of relevant functional features on a highlighted GO direct acyclic graph (DAG). Furthermore B2G includes various statistics charts summarizing the results obtained at BLASTing, GO-mapping, annotation and enrichment analysis (Fisher''''s Exact Test). All analysis process steps are configurable and data import and export are supported at any stage. The application also accepts pre-existing BLAST or annotation files and takes them to subsequent steps. The tool offers a very suitable platform for high throughput functional genomics research in non-model species. B2G is a species-independent, intuitive and interactive desktop application which allows monitoring and comprehending the whole annotation and analysis process supported by additional features like GO Slim integration, evidence code (EC) consideration, a Batch-Mode or GO-Multilevel-Pies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | annotation, visualization, analysis, functional genomics, editor, statistical analysis, slimmer-type tool, ontology or annotation editor, functional analysis, direct acyclic graph, analysis, high throughput, functional genomics |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: Principe Felipe Research Centre; Valencia; Spain |
MCyT GEN 2001 - 4885-C05-03; eTumour Project FP6-2002-LIFESCIHEALTH 503094 |
PMID:16081474 | Free for academic use | OMICS_01475, nlx_149335 | SCR_005828 | Blast2GO (B2G) | 2026-08-04 09:41:27 | 8422 | |||||
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AltAnalyze - Alternative Splicing Analysis Tool Resource Report Resource Website 50+ mentions |
AltAnalyze - Alternative Splicing Analysis Tool (RRID:SCR_002951) | AltAnalyze | software application, software resource | Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph. | analysis, alternative splicing, microarray, calculate, pathway, ontology, domain, microrna, targeting, splicing, microarry, rna-seq, metabolomics, mac osx, windows, ubuntu, cross platform, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Cytoscape has parent organization: University of California at San Francisco; California; USA |
PMID:20513647 | Free, Available for download, Freely available | nif-0000-30083, OMICS_02250, biotools:altanalyze | https://bio.tools/altanalyze | SCR_002951 | Alternative Splicing Analysis Tool | 2026-08-04 09:40:46 | 81 | |||||
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SPHARM-MAT Resource Report Resource Website 1+ mentions |
SPHARM-MAT (RRID:SCR_002545) | SPHARM-MAT | software application, software resource, software toolkit | A matlab-based 3D shape modeling and analysis toolkit, and is designed to aid statistical shape analysis for identifying morphometric changes in 3D structures of interest related to different conditions. SPHARM-MAT is implemented based on a powerful 3D Fourier surface representation method called SPHARM, which creates parametric surface models using spherical harmonics. | analyze, c, matlab, microsoft, morphology, magnetic resonance, nifti, posix/unix-like, quantification, quantitative shape analysis, shape analysis, shape decomposition, spherical harmonics, surface analysis, win32 (ms windows), windows, parametric surface model, spherical harmonics, 3d, shape modeling, analysis, morphometry |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Indiana University School of Medicine; Indiana; USA |
NIBIB R03EB008674-01 | Free, Available for download, Freely available | nlx_155952 | http://www.nitrc.org/projects/spharm-mat | SCR_002545 | 2026-08-04 09:40:40 | 2 | ||||||
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Bioconductor Resource Report Resource Website 10000+ mentions |
Bioconductor (RRID:SCR_006442) | software toolkit, software resource, software repository | Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data. | catalog, analysis, genomic, metadata, comprehension, statistical, data |
lists: MSstats lists: MetaCyto lists: MetaNeighbor lists: tximport lists: clusterProfiler lists: ropls lists: FlowSOM lists: scran lists: Rsubread lists: riboSeqR lists: Biostrings lists: ConsensusClusterPlus lists: DESeq2 lists: GenomicFeatures lists: affy lists: affydata lists: Genomic Ranges lists: Goseq lists: GAGE lists: CATALYST lists: Scmap lists: Scfind lists: GenomicRanges lists: org.Rn.eg.db lists: Extending Guilt by Association by Degree lists: ggtree lists: StructuralVariantAnnotation lists: scTHI lists: EnhancedVolcano lists: DEGreport lists: variancePartition lists: biomaRt lists: MSnbase lists: ReactomePA lists: SynergyFinder lists: CiteFuse lists: fgsea lists: GSVA lists: SimFFPE lists: FilterFFPE lists: PhenStat lists: ChIPseeker lists: AUCell lists: svaNUMT lists: KEGGgraph lists: epialleleR lists: microbiome lists: Orthology.eg.db lists: org.Hs.eg.db lists: ExperimentHub lists: combi is listed by: OMICtools is listed by: Gene Ontology Tools is listed by: SoftCite is affiliated with: RnaSeqGeneEdgeRQL is related to: asSeq is related to: Gene Ontology is related to: CRCView is related to: R Project for Statistical Computing is related to: GEO2R is related to: LIMMA is related to: VisR is related to: edgeR is related to: IMEx - The International Molecular Exchange Consortium is related to: CATALYSTLite is related to: ascend is related to: minet has parent organization: Fred Hutchinson Cancer Center is parent organization of: ncdfFlow is parent organization of: GenomicRanges is parent organization of: ReadqPCR is parent organization of: flowCL is parent organization of: flowBin is parent organization of: CorMut is parent organization of: metaSeq is parent organization of: VariantAnnotation is parent organization of: ReQON is parent organization of: timecourse is parent organization of: RmiR.Hs.miRNA is parent organization of: AffyRNADegradation is parent organization of: ArrayExpress (R) is parent organization of: GEOquery is parent organization of: MIMOSA is parent organization of: HEM is parent organization of: CNTools is parent organization of: cn.FARMS is parent organization of: Clonality is parent organization of: TransView is parent organization of: pvac is parent organization of: QUALIFIER is parent organization of: flowStats is parent organization of: rTANDEM is parent organization of: flowFlowJo is parent organization of: iASeq is parent organization of: OLINgui is parent organization of: SigFuge is parent organization of: Rdisop is parent organization of: GeneExpressionSignature is parent organization of: iBMQ is parent organization of: TDARACNE is parent organization of: flowQ is parent organization of: FlipFlop is parent organization of: RmiR is parent organization of: bsseq is parent organization of: ExomePeak is parent organization of: flowWorkspace is parent organization of: massiR is parent organization of: rbsurv is parent organization of: GeneMeta is parent organization of: MergeMaid is parent organization of: categoryCompare is parent organization of: metahdep is parent organization of: snpStats: SnpMatrix and XSnpMatrix classes and methods is parent organization of: CNVtools is parent organization of: CGEN is parent organization of: RCASPAR is parent organization of: iterativeBMAsurv is parent organization of: multtest is parent organization of: globaltest is parent organization of: MinimumDistance is parent organization of: VegaMC is parent organization of: VanillaICE is parent organization of: SNPchip is parent organization of: SMAP is parent organization of: quantsmooth is parent organization of: mBPCR is parent organization of: ITALICS is parent organization of: GenoSet is parent organization of: exomeCopy is parent organization of: CGHregions is parent organization of: CGHbase is parent organization of: beadarraySNP is parent organization of: GLAD is parent organization of: methylMnM is parent organization of: methyAnalysis is parent organization of: ARRmNormalization is parent organization of: ChIPsim is parent organization of: yaqcaffy is parent organization of: wateRmelon is parent organization of: sRAP is parent organization of: spotSegmentation is parent organization of: SNM is parent organization of: SNAGEE is parent organization of: Simpleaffy is parent organization of: qcmetrics is parent organization of: MANOR is parent organization of: limmaGUI is parent organization of: ffpe is parent organization of: dyebias is parent organization of: DEXUS is parent organization of: BeadDataPackR is parent organization of: aroma.light is parent organization of: ArrayTools is parent organization of: beadarray is parent organization of: arrayQuality is parent organization of: arrayMvout is parent organization of: affyQCReport is parent organization of: affyPLM is parent organization of: AffyExpress is parent organization of: waveTiling is parent organization of: gprege is parent organization of: oneChannelGUI is parent organization of: LMGene is parent organization of: factDesign is parent organization of: pickgene is parent organization of: betr is parent organization of: SCAN.UPC is parent organization of: arrayQualityMetrics is parent organization of: CALIB is parent organization of: DEDS is parent organization of: Harshlight is parent organization of: MiChip is parent organization of: OCplus is parent organization of: bridge is parent organization of: fRMA is parent organization of: genArise is parent organization of: lapmix is parent organization of: maCorrPlot is parent organization of: maSigPro is parent organization of: MACAT is parent organization of: maigesPack is parent organization of: MDQC is parent organization of: metaArray is parent organization of: nnNorm is parent organization of: plgem is parent organization of: PVCA is parent organization of: RAMA is parent organization of: stepNorm is parent organization of: virtualArray is parent organization of: LPE is parent organization of: vsn is parent organization of: ACME is parent organization of: CoGAPS is parent organization of: flowFP is parent organization of: rMAT is parent organization of: SLqPCR is parent organization of: nondetects is parent organization of: unifiedWMWqPCR is parent organization of: sSeq is parent organization of: CNVrd2 is parent organization of: plateCore is parent organization of: RSVSim is parent organization of: TCC is parent organization of: CQN is parent organization of: COMPASS is parent organization of: flowClust is parent organization of: SPADE is parent organization of: OrderedList is parent organization of: SamSPECTRAL is parent organization of: flowUtils is parent organization of: RchyOptimyx is parent organization of: TEQC is parent organization of: flowType is parent organization of: ADaCGH2 is parent organization of: flowViz is parent organization of: flowTrans is parent organization of: flowQB is parent organization of: shinyTANDEM is parent organization of: flowPlots is parent organization of: flowPhyto is parent organization of: flowCore is parent organization of: flowMerge is parent organization of: flowMap is parent organization of: flowMeans is parent organization of: spliceR is parent organization of: flowMatch is parent organization of: flowFit is parent organization of: flowCyBar is parent organization of: BEAT is parent organization of: flowBeads is parent organization of: CAMERA - Collection of annotation related methods for mass spectrometry data is parent organization of: MBASED is parent organization of: MethylAid is parent organization of: sapFinder is parent organization of: Pathview is parent organization of: DSS is parent organization of: RMassBank is parent organization of: iontree is parent organization of: Basic4Cseq is parent organization of: BiGGR is parent organization of: mzR is parent organization of: PAPi is parent organization of: CGHnormaliter is parent organization of: Chimera is parent organization of: BRAIN is parent organization of: tweeDEseq is parent organization of: SurvComp is parent organization of: Triplex is parent organization of: OmicCircos is parent organization of: ggbio is parent organization of: HTqPCR is parent organization of: NormqPCR is parent organization of: ddCt is parent organization of: EasyqpcR is parent organization of: SWAN is parent organization of: PING is parent organization of: DMRforPairs is parent organization of: SeqGSEA is parent organization of: h5vc is parent organization of: deepSNV is parent organization of: RUVSeq is parent organization of: BHC is parent organization of: epigenomix is parent organization of: IRanges is parent organization of: GeneNetworkBuilder is parent organization of: MethylSeekR is parent organization of: SRAdb is parent organization of: casper is parent organization of: htSeqTools is parent organization of: ChIPXpress is parent organization of: methVisual is parent organization of: DeconRNASeq is parent organization of: EDASeq is parent organization of: RIPSeeker is parent organization of: ShortRead is parent organization of: seqbias is parent organization of: DEGseq is parent organization of: arrayMagic is parent organization of: easyRNASeq is parent organization of: DNAcopy is parent organization of: CRLMM is parent organization of: motifRG is parent organization of: MMDiff is parent organization of: MiRaGE is parent organization of: LVSmiRNA is parent organization of: ExiMiR is parent organization of: RPA is parent organization of: CexoR is parent organization of: lumi is parent organization of: baySeq is parent organization of: tRanslatome is parent organization of: DNaseR is parent organization of: DEXSeq is parent organization of: ChIPpeakAnno is parent organization of: inSilicoMerging is parent organization of: minfi is parent organization of: Methylumi is parent organization of: miRNApath is parent organization of: sva package is parent organization of: dmrFinder is parent organization of: rqubic is parent organization of: BicARE is parent organization of: iBBiG is parent organization of: eisa is parent organization of: ChAMP is parent organization of: cghMCR is parent organization of: Bioconductor mailing list is parent organization of: DiffBind is parent organization of: NarrowPeaks is parent organization of: CSAR is parent organization of: CSSP is parent organization of: TargetScore is parent organization of: snapCGH is parent organization of: iChip is parent organization of: TurboNorm is parent organization of: Ringo is parent organization of: RLMM is parent organization of: charm is parent organization of: BiSeq is parent organization of: MEDME is parent organization of: MEDIPS is parent organization of: BayesPeak is parent organization of: ChIPseqR is parent organization of: Rolexa is parent organization of: cn.mops is parent organization of: RankProd is parent organization of: phyloseq is parent organization of: HiTC is parent organization of: CancerMutationAnalysis is parent organization of: aCGH is parent organization of: Repitools is parent organization of: flowPeaks is parent organization of: Mfuzz is parent organization of: les is parent organization of: OLIN is parent organization of: affylmGUI is parent organization of: CYCLE is parent organization of: r3Cseq is parent organization of: Piano is parent organization of: RamiGO hosts: DESeq hosts: rGADEM hosts: PICS hosts: Jmosaics hosts: R453Plus1Toolbox hosts: BAC hosts: targetscan.Hs.eg.db hosts: Starr hosts: Qvalue hosts: topGO hosts: MmPalateMiRNA hosts: CGHcall hosts: EGSEA hosts: NOISeq |
Catt Family Foundation ; Dana Farber Cancer Institute ; NHGRI R33 HG002708 |
PMID:15461798 | Free, Freely available | OMICS_01759, nif-0000-10445 | SCR_006442 | 2026-08-04 09:41:36 | 22974 | |||||||
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Nipype Resource Report Resource Website 500+ mentions |
Nipype (RRID:SCR_002502) | Nipype | software application, software resource | A package for writing fMRI analysis pipelines and interfacing with external analysis packages (SPM, FSL, AFNI). Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of Nipy, is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems. | magnetic resonance, python, workflow, analysis, pipeline, interface, data processing, neuroimaging |
is used by: Forward: Accurate finite element electromagnetic head models is used by: fMRIPrep is used by: NHP BIDS is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuroimaging in Python |
PMID:21897815 | Free, Available for download, Freely available | nlx_155901 | http://www.nitrc.org/projects/nipype | SCR_002502 | Nipype: Neuroimaging in Python Pipeline and Interfaces, NIPY Pipeline and Interfaces | 2026-08-04 09:40:40 | 822 | |||||
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Phenotypes and Mutant Alleles Resource Report Resource Website 10+ mentions |
Phenotypes and Mutant Alleles (RRID:SCR_017523) | database, data or information resource, service resource | Enables comparative phenotype analysis, searches for human disease models, and hypothesis generation by providing access to spontaneous, induced, and genetically engineered mutations and their strain-specific phenotypes. | MGI, phenotype, human, disease, analysis, model, genetically, engineered, mutation, strain, specific, phenotype, data | has parent organization: Mouse Genome Informatics (MGI) | Free, Freely available | SCR_017523 | Phenotypes, Alleles & Disease Models | 2026-08-04 09:44:14 | 11 | |||||||||
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C. elegans RNAi Collection (Ahringer) Resource Report Resource Website 10+ mentions |
C. elegans RNAi Collection (Ahringer) (RRID:SCR_017064) | database, data or information resource | C. elegans RNAi feeding library distributed by Source BioScience Ltd. Designed for genome wide study of gene function in C. elegans through loss of function studies. | Source BioScience Ltd, data, collection, bacterial, strain, Caenorhabditis elegans, RNA, interference, RNAi, gene, function, analysis, feeding, library | has parent organization: University of Cambridge; Cambridge; United Kingdom | Howard Hughes Medical Institute Predoctoral Fellow- ship ; Wellcome Trust Senior Research Fellowship |
PMID:12828945 | Available for purchase | SCR_017064 | 2026-08-04 09:44:04 | 14 | ||||||||
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University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility Resource Report Resource Website |
University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility (RRID:SCR_017168) | MidSouth Bioinformatics Center, MBC | access service resource, software resource, core facility, service resource | Core provides bioinformatics consulting, training, technical assistance, and access to computational infrastructure for faculty, students, and researchers in region with their bioscience computational needs. Offers private sessions, workshops and training on specialty topics. Computing resources including software, computing cluster, technical advice. | bioinformatics, assistance, consulting, training, analysis, omic, data | has parent organization: University of Arkansas; Arkansas; USA | Open | SCR_017168 | Bioinformatics Center, , University of Arkansas, UA, Core Facility, MBC, UALR, MidSouth, Little Rock | 2026-08-04 09:44:07 | 0 |
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