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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RamiGO Resource Report Resource Website 10+ mentions |
RamiGO (RRID:SCR_006922) | RamiGO | software resource | Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape. | visualization, analysis, ontology or annotation search engine, ontology or annotation visualization, other analysis, classification, go, graph, network, third party client, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: Cytoscape is related to: AmiGO has parent organization: Dana-Farber Cancer Institute has parent organization: Bioconductor |
PMID:23297033 | Artistic License, v2 | biotools:ramigo, OMICS_02267, nlx_149331 | http://bioconductor.org/packages/release/bioc/html/RamiGO.html https://bio.tools/ramigo |
SCR_006922 | ramigo, RamiGO - AmiGO visualize R interface | 2026-02-14 02:01:15 | 11 | |||||
|
Gene Ontology Tools Resource Report Resource Website 10+ mentions |
Gene Ontology Tools (RRID:SCR_006941) | GO Tools | software repository, catalog, data or information resource, software resource, database | Collection of tools developed by GO Consortium and by third parties. Tools are listed by category or alphabetically and continue to be improved and expanded. | registry, annotation browser, annotation search engine, annotation visualization, ontology, annotation editor, database, data warehouse, software library, statistical analysis, slimmer-type tool, term enrichment, text mining, protein interaction, functional similarity, semantic similarity, analysis, annotation, visualization, editor |
lists: GOALIE lists: GenNav lists: High-Throughput GoMiner lists: Onto-Design lists: Avadis lists: GONUTS lists: PiNGO lists: TM4 Microarray Software Suite - TIGR MultiExperiment Viewer lists: FunSimMat lists: BioPerl lists: Database for Annotation Visualization and Integrated Discovery lists: GOToolBox Functional Investigation of Gene Datasets lists: StRAnGER lists: Short Time-series Expression Miner (STEM) lists: GORetriever lists: Gene Ontology Browsing Utility (GOBU) lists: GeneTools lists: GOSlimViewer lists: go-moose lists: Network Ontology Analysis lists: OBO-Edit lists: Onto-Compare lists: Onto-Express lists: OntoVisT lists: STRAP lists: CGAP GO Browser lists: COBrA lists: Gene Class Expression lists: GeneInfoViz lists: GOfetcher lists: GoFish lists: GOProfiler lists: GOanna lists: Manatee lists: Pandora - Protein ANnotation Diagram ORiented Analysis lists: TAIR Keyword Browser lists: Wandora lists: GeneMANIA lists: GOTaxExplorer lists: go-db-perl lists: Onto-Miner lists: Onto-Translate lists: ToppGene Suite lists: DBD - Slim Gene Ontology lists: go-perl lists: ONTO-PERL lists: OWLTools lists: Blip: Biomedical Logic Programming lists: OWL API lists: CLENCH lists: BiNGO: A Biological Networks Gene Ontology tool lists: CateGOrizer lists: FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products lists: ProteInOn lists: GeneMerge lists: GraphWeb lists: ClueGO lists: CLASSIFI - Cluster Assignment for Biological Inference lists: GOHyperGAll lists: FuncAssociate: The Gene Set Functionator lists: GOdist lists: FuncExpression lists: FunCluster lists: FIVA - Functional Information Viewer and Analyzer lists: GARBAN lists: GOEx - Gene Ontology Explorer lists: SGD Gene Ontology Slim Mapper lists: GOArray lists: GoSurfer lists: GOtcha lists: MAPPFinder lists: GoAnnotator lists: MetaGeneProfiler lists: OntoGate lists: ProfCom - Profiling of complex functionality lists: SerbGO lists: SOURCE lists: Ontologizer lists: THEA - Tools for High-throughput Experiments Analysis lists: Generic GO Term Mapper lists: GREAT: Genomic Regions Enrichment of Annotations Tool lists: GoBean - a Java application for Gene Ontology enrichment analysis lists: TXTGate lists: GO-Module lists: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures lists: G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools lists: Expression Profiler lists: GOChase lists: Whatizit lists: REViGO lists: WEGO - Web Gene Ontology Annotation Plot lists: Blast2GO lists: InterProScan lists: PubSearch lists: GO Online SQL Environment (GOOSE) lists: Gene Ontology For Functional Analysis (GOFFA) lists: MGI GO Browser lists: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit lists: Ontology Lookup Service lists: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit lists: g:Profiler lists: OwlSim lists: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool lists: FastSemSim lists: RamiGO lists: GeneCodis lists: FunSpec lists: FunNet - Transcriptional Networks Analysis lists: agriGO lists: GOblet lists: DynGO lists: SeqExpress lists: ProbeExplorer lists: GOstat lists: Onto-Express To Go (OE2GO) lists: Tk-GO lists: Spotfire lists: GOMO - Gene Ontology for Motifs lists: GFINDer: Genome Function INtegrated Discoverer lists: Agile Protein Interactomes DataServer lists: elk-reasoner lists: Flash Gviewer lists: L2L Microarray Analysis Tool lists: OnEx - Ontology Evolution Explorer lists: Semantic Measures Library lists: AmiGO lists: Babelomics lists: T-profiler lists: QuickGO lists: FSST - Functional Similarity Search Tool lists: GoPubMed lists: Bioconductor lists: ErmineJ lists: Comparative Toxicogenomics Database (CTD) lists: LexGrid lists: Candidate Genes to Inherited Diseases lists: EGAN: Exploratory Gene Association Networks lists: Generic GO Term Finder lists: Integrated Manually Extracted Annotation lists: EASE: the Expression Analysis Systematic Explorer is listed by: NIF Data Federation has parent organization: Gene Ontology |
Free, Freely available | nlx_146273 | https://neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_146273-1 | http://www.geneontology.org/GO.tools.shtml | SCR_006941 | 2026-02-14 02:01:15 | 27 | ||||||
|
MSstats Resource Report Resource Website 100+ mentions |
MSstats (RRID:SCR_014353) | data analysis software, software resource, data processing software, software application | A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations. | data independent acquisition, statistical relative quantification, protein, peptide, data analysis software, data processing, data visualization, proteomics |
uses: R Project for Statistical Computing is used by: Skyline is listed by: Bioconductor |
National Science Foundation CAREER award 1054826 | DOI:10.1186/1471-2105-13-S16-S6 | Acknowledgement requested, Available for download | http://www.bioconductor.org/packages/release/bioc/html/MSstats.html | SCR_014353 | MSStats | 2026-02-14 02:02:40 | 214 | ||||||
|
SeqGSEA Resource Report Resource Website 10+ mentions |
SeqGSEA (RRID:SCR_005724) | SeqGSEA | data analysis software, software resource, data processing software, software application | Software package that provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene''s differential expression and splicing, respectively. | differential expression, gene expression, gene set enrichment, rna-seq, sequencing, splicing |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v3 or newer | OMICS_02251 | SCR_005724 | SeqGSEA - Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing | 2026-02-14 02:01:09 | 34 | |||||||
|
deepSNV Resource Report Resource Website 10+ mentions |
deepSNV (RRID:SCR_006214) | deepSNV | software resource | Software package that provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs (single nucleotide variants). | data import, genetic variability, genetics, snp, sequencing, single nucleotide variant, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24443148 | GNU General Public License, v3 | OMICS_02239, biotools:deepsnv | https://bio.tools/deepsnv | SCR_006214 | deepSNV - Detection of subclonal SNVs in deep sequencing experiments | 2026-02-14 02:01:06 | 34 | |||||
|
MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | data processing software, data analysis software, software toolkit, software application, software resource | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | 2026-02-14 02:03:15 | 5 | |||||||
|
bsseq Resource Report Resource Website 1+ mentions |
bsseq (RRID:SCR_001072) | sequence analysis software, data processing software, data analysis software, software application, software resource | R package with tools for analyzing and visualizing bisulfite sequencing data. | bisulfite sequencing, analyze, r, sequence analysis software, data analysis software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01847, biotools:bsseq | https://bio.tools/bsseq | SCR_001072 | bsseq - Analyze manage and store bisulfite sequencing data | 2026-02-14 01:59:54 | 8 | |||||||
|
MmPalateMiRNA Resource Report Resource Website 1+ mentions |
MmPalateMiRNA (RRID:SCR_001070) | data processing software, data analysis software, source code, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software R package written for analysis of murine palate miRNA two-color expression data. | murine, palate, mirna, two color expression, open source, r |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:23298515 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00788 | SCR_001070 | 2026-02-14 01:59:54 | 1 | ||||||||
|
R453Plus1Toolbox Resource Report Resource Website 1+ mentions |
R453Plus1Toolbox (RRID:SCR_001105) | sequence analysis software, data processing software, data analysis software, software toolkit, software application, software resource | R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided. | genome, sequence, visualization, structural variants, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:21349869 | Free, Available for download, Freely available | OMICS_01354 | SCR_001105 | 2026-02-14 01:59:53 | 4 | ||||||||
|
RmiR Resource Report Resource Website |
RmiR (RRID:SCR_001069) | RmiR | sequence analysis software, data processing software, data analysis software, software application, software resource | R package that contains functions to merge microRNA and respective targets using different databases. | micro rna, mrna, function, target, r, sequence analysis software |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00789 | https://rdrr.io/bioc/RmiR/ | SCR_001069 | 2026-02-14 01:59:58 | 0 | |||||||
|
Jmosaics Resource Report Resource Website |
Jmosaics (RRID:SCR_001094) | sequence analysis software, data processing software, data analysis software, software application, software resource | R software that detects enriched regions of ChIP-seq data sets jointly. | chip seq, data, genomics, sequencing, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00445 | SCR_001094 | 2026-02-14 01:59:59 | 0 | |||||||||
|
massiR Resource Report Resource Website |
massiR (RRID:SCR_001157) | software resource | Software that predicts the sex of samples in gene expression microarray datasets. | standalone software, mac os x, unix/linux, windows, r, classification, clustering, gene expression, microarray, quality control, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24659105 | Free, Available for download, Freely available | biotools:massir, OMICS_03638 | https://bio.tools/massir | SCR_001157 | massiR: MicroArray Sample Sex Identifier, MicroArray Sample Sex Identifier | 2026-02-14 01:59:56 | 0 | ||||||
|
yaqcaffy Resource Report Resource Website 1+ mentions |
yaqcaffy (RRID:SCR_001295) | yaqcaffy | software resource | Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets. | microarray, one channel, quality control, report writing, affymetrix, gene expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | BioTools:yaqcaffy, biotools:yaqcaffy, OMICS_02040 | http://www.bioconductor.org/packages/release/bioc/html/yaqcaffy.html | SCR_001295 | yaqcaffy - Affymetrix expression data quality control and reproducibility analysis | 2026-02-14 01:59:58 | 2 | ||||||
|
ChIPsim Resource Report Resource Website 1+ mentions |
ChIPsim (RRID:SCR_001293) | ChIPsim | software resource | Software package providing a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments. | chip-seq, infrastructure, simulation |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 or newer | OMICS_02042 | SCR_001293 | ChIPsim - Simulation of ChIP-seq experiments | 2026-02-14 02:00:05 | 1 | |||||||
|
methyAnalysis Resource Report Resource Website 1+ mentions |
methyAnalysis (RRID:SCR_001290) | methyAnalysis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focuses on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data. | dna methylation, microarray, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21159174 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02046 | SCR_001290 | methyAnalysis - DNA methylation data analysis and visualization | 2026-02-14 01:59:59 | 9 | ||||||
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les Resource Report Resource Website |
les (RRID:SCR_001291) | les | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes. | loci of enhanced significance, tiling microarray, tiling, microarray, chip-chip, dna modification, probe, dna methylation, differential expression, microarray, transcription, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:les, OMICS_02045 | https://bioconductor.org/packages/les/ https://bio.tools/les |
SCR_001291 | les package: Identifying Differential Effects in Tiling Microarray Data, Loci of Enhanced Significance | 2026-02-14 01:59:57 | 0 | ||||||
|
beadarraySNP Resource Report Resource Website |
beadarraySNP (RRID:SCR_001281) | beadarraySNP | software resource | Software package for importing data from Illumina SNP experiments and performing copy number calculations and reports. | copy number variation, data import, genetic variability, preprocessing, snp, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02056 | http://www.bioconductor.org/packages/devel/bioc/html/beadarraySNP.html | SCR_001281 | beadarraySNP - Normalization and reporting of Illumina SNP bead arrays | 2026-02-14 01:59:59 | 0 | ||||||
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RCASPAR Resource Report Resource Website |
RCASPAR (RRID:SCR_001253) | RCASPAR | software resource | Software package for survival time prediction based on a piecewise baseline hazard Cox regression model. It is meant to help predict survival times in the presence of high-dimensional explanatory covariates. | gene expression, genetics, proteomics, visualization, acgh |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02087 | SCR_001253 | 2026-02-14 01:59:58 | 0 | ||||||||
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CNVtools Resource Report Resource Website 10+ mentions |
CNVtools (RRID:SCR_001250) | CNVtools | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies. | genetic variability, copy number variant, genetic association |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18776912 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02090 | SCR_001250 | CNVtools - A package to test genetic association with CNV data | 2026-02-14 01:59:56 | 12 | ||||||
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CGEN Resource Report Resource Website 10+ mentions |
CGEN (RRID:SCR_001251) | CGEN | data analysis software, software resource, data processing software, software application | Software R package for analysis of case-control studies in genetic epidemiology. | genetic, epidemiology, r, case-control, clustering, multiple comparison, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:21387464 | Free, Available for download, Freely available | OMICS_02089 | SCR_001251 | CGEN - An R package for analysis of case-control studies in genetic epidemiology | 2026-02-14 01:59:59 | 17 |
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