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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data analysis software, data processing software, software application, software resource | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool, https://bio.tools/limma, https://sources.debian.org/src/r-bioc-limma/ | SCR_010943 | Linear Models for Microarray Data | 2026-09-05 06:26:50 | 27197 | ||||||
|
EDASeq Resource Report Resource Website 100+ mentions |
EDASeq (RRID:SCR_006751) | EDASeq | software resource | Software for numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis, normalization, rna-seq |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01231 | SCR_006751 | EDASeq: Exploratory Data Analysis and Normalization for RNA-Seq data | 2026-09-05 06:26:00 | 255 | |||||||
|
ShortRead Resource Report Resource Website 100+ mentions |
ShortRead (RRID:SCR_006813) | ShortRead | software resource | Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats. | high throughput sequence data, short read, DNA sequences, short read data |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: Bioconductor |
PMID:19654119 | Free, Available for download, Freely available | OMICS_01076 | https://sources.debian.org/src/r-bioc-shortread/ | SCR_006813 | ShortRead - Classes and methods for high-throughput short-read sequencing data. | 2026-09-05 06:26:01 | 235 | |||||
|
RIPSeeker Resource Report Resource Website 10+ mentions |
RIPSeeker (RRID:SCR_006810) | RIPSeeker | software resource | A statistical software package for identifying protein-associated transcripts from RIP-seq experiments. Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation. | rip-seq |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 | OMICS_00569 | SCR_006810 | RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments | 2026-09-05 06:26:01 | 12 | |||||||
|
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 | 2026-09-05 06:26:03 | 12 | |||||
|
Gene Ontology Tools Resource Report Resource Website 10+ mentions |
Gene Ontology Tools (RRID:SCR_006941) | GO Tools | catalog, data or information resource, database, software repository, software resource | 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 | 2026-09-05 06:26:04 | 27 | ||||||
|
iASeq Resource Report Resource Website |
iASeq (RRID:SCR_000420) | software resource | Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins. | software package, unix/linux, mac os x, windows, r, chip-seq, rna-seq, snp |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23194258 | Free, Available for download, Freely available | OMICS_05505 | SCR_000420 | iASeq: integrating multiple sequencing datasets for detecting allele-specific events | 2026-09-05 06:24:19 | 0 | |||||||
|
rTANDEM Resource Report Resource Website |
rTANDEM (RRID:SCR_000409) | software resource | An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, proteomics |
is used by: shinyTANDEM is listed by: OMICtools has parent organization: Bioconductor |
PMID:24700319 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_03516 | SCR_000409 | rTANDEM - Interfaces the tandem protein identification algorithm in R | 2026-09-05 06:24:19 | 0 | |||||||
|
flowPeaks Resource Report Resource Website |
flowPeaks (RRID:SCR_000407) | software resource | Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry, gating, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:22595209 | Free, Available for download, Freely available | biotools:flowpeaks, OMICS_05604 | http://www.bioconductor.org/packages/devel/bioc/html/flowPeaks.html, https://bio.tools/flowpeaks | SCR_000407 | 2026-09-05 06:24:20 | 0 | |||||||
|
QUALIFIER Resource Report Resource Website |
QUALIFIER (RRID:SCR_000389) | software resource | Software that provides quality control and quality assessment tools for gated flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23020243 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05618 | SCR_000389 | QUALIFIER - Quality Control of Gated Flow Cytometry Experiments | 2026-09-05 06:24:18 | 0 | |||||||
|
TDARACNE Resource Report Resource Website |
TDARACNE (RRID:SCR_000498) | TDARACNE | software resource | Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data. | microarray, time course |
is listed by: OMICtools has parent organization: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02013 | SCR_000498 | TDARACNE - Network reverse engineering from time course data | 2026-09-05 06:24:21 | 0 | |||||||
|
Mfuzz Resource Report Resource Website 10+ mentions |
Mfuzz (RRID:SCR_000523) | software resource | Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | r, time series, gene expression, clustering, microarray, preprocessing, time course, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:18084642 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mfuzz, OMICS_02012 | https://bio.tools/mfuzz | http://itb.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/ | SCR_000523 | Mfuzz - Soft clustering of time series gene expression data | 2026-09-05 06:24:21 | 16 | |||||
|
Rdisop Resource Report Resource Website |
Rdisop (RRID:SCR_000453) | software resource | Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02416, biotools:rdisop | https://github.com/sneumann/Rdisop, https://bio.tools/rdisop | SCR_000453 | Rdisop - Decomposition of Isotopic Patterns, Rdisop: Decomposition of Isotopic Patterns, Decomposition of Isotopic Patterns | 2026-09-05 06:24:19 | 0 | |||||||
|
FlipFlop Resource Report Resource Website |
FlipFlop (RRID:SCR_000625) | software resource | Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data. | standalone software, unix/linux, mac os x, windows, r, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:24813214 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04028, biotools:flipflop | https://bio.tools/flipflop | SCR_000625 | flipflop - Fast lasso-based isoform prediction as a flow problem | 2026-09-05 06:24:22 | 0 | ||||||
|
bsseq Resource Report Resource Website 1+ mentions |
bsseq (RRID:SCR_001072) | data analysis software, data processing software, sequence 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 | 2026-09-05 06:24:29 | 8 | |||||||
|
MmPalateMiRNA Resource Report Resource Website 1+ mentions |
MmPalateMiRNA (RRID:SCR_001070) | data analysis software, data processing software, software application, software resource, source code | 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 | 2026-09-05 06:24:29 | 1 | ||||||||
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R453Plus1Toolbox Resource Report Resource Website 1+ mentions |
R453Plus1Toolbox (RRID:SCR_001105) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | 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 | 2026-09-05 06:24:29 | 4 | ||||||||
|
RmiR Resource Report Resource Website |
RmiR (RRID:SCR_001069) | RmiR | data analysis software, data processing software, sequence 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 | 2026-09-05 06:24:29 | 0 | |||||||
|
Jmosaics Resource Report Resource Website |
Jmosaics (RRID:SCR_001094) | data analysis software, data processing software, sequence 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 | 2026-09-05 06:24:29 | 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 | 2026-09-05 06:24:30 | 0 |
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