Searching the RRID Resource Information Network
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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
genArise Resource Report Resource Website 10+ mentions |
genArise (RRID:SCR_001346) | genArise | data analysis software, software application, data processing software, software resource | An easy to use software tool for dual color microarray data. Its GUI-Tk based environment lets any non-experienced user perform a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer. | microarray, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely Available | OMICS_01993 | SCR_001346 | genArise - Microarray Analysis tool | 2026-02-17 09:59:35 | 22 | |||||||
|
categoryCompare Resource Report Resource Website 1+ mentions |
categoryCompare (RRID:SCR_001223) | categoryCompare | data analysis software, software application, data processing software, software resource | A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested). | annotation, go, gene expression, multiple comparison, pathway, gene |
uses: Cytoscape is listed by: OMICtools is related to: Gene Ontology is related to: CRAN has parent organization: Bioconductor |
PMID:24808906 | Free, Available for download, Freely available | OMICS_02122 | SCR_001223 | categoryCompare - Meta-analysis of high-throughput experiments using feature annotations | 2026-02-17 09:59:35 | 9 | ||||||
|
BAC Resource Report Resource Website |
BAC (RRID:SCR_001067) | BAC | software application, data processing software, data analysis software, software resource, sequence analysis software | R software package that uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments. | software, bayesian, chip, hierarchy, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00801 | SCR_001067 | 2026-02-17 09:59:34 | 0 | ||||||||
|
targetscan.Hs.eg.db Resource Report Resource Website |
targetscan.Hs.eg.db (RRID:SCR_001068) | software application, data processing software, data analysis software, software resource, sequence analysis software | R software that predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. | software, biological targets, mirna, prediction, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00790 | SCR_001068 | 2026-02-17 09:59:35 | 0 | |||||||||
|
globaltest Resource Report Resource Website 10+ mentions |
globaltest (RRID:SCR_001256) | globaltest | software application, data processing software, data analysis software, software resource, sequence analysis software | A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms. | differential expression, go, microarray, one channel, pathway, bio.tools |
uses: KEGG is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Bioconductor |
PMID:34046931 | Free, Available for download, Freely available | biotools:globaltest, OMICS_02084 | https://bio.tools/globaltest | SCR_001256 | 2026-02-17 09:59:35 | 30 | ||||||
|
rGADEM Resource Report Resource Website |
rGADEM (RRID:SCR_001091) | software application, data processing software, data analysis software, software resource, sequence analysis software | R package with tools for de novo motif discovery in large-scale genomic sequence data. | de novo motif, genomics, sequencing, data, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00491 | SCR_001091 | 2026-02-17 09:59:33 | 0 | |||||||||
|
MinimumDistance Resource Report Resource Website |
MinimumDistance (RRID:SCR_001260) | MinimumDistance | data analysis software, software application, data processing software, software resource | Software package for analysis of de novo copy number variants in trios from high-dimensional genotyping platforms. | copy number variation, microarray, snp |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02066 | SCR_001260 | MinimumDistance - A package for de novo CNV detection in case-parent trios | 2026-02-17 09:59:37 | 0 | |||||||
|
SimFFPE Resource Report Resource Website 1+ mentions |
SimFFPE (RRID:SCR_021085) | software application, software resource, simulation software | Software R package to simulate artifact chimeric reads specifically generated in next generation sequencing process of formalin fixed paraffin embedded tissue. Simulates normal reads as well as artifact chimeric reads that are enriched in FFPE samples. These artifact chimeric reads can lead to large amounts of false positive structural variant calls. | FFPE, NGS read simulator, artifact chimeric read, next generation sequencing process, normal reads simulation, artifact chimeric reads simulation, formalin fixed paraffin embedded tissue, |
is listed by: Bioconductor is related to: CRAN |
Free, Available for download, Freely available | SCR_021085 | NGS Read Simulator for FFPE Tissue, Simulator for FFPE Tissue | 2026-02-16 09:49:56 | 1 | |||||||||
|
KEGGgraph Resource Report Resource Website 10+ mentions |
KEGGgraph (RRID:SCR_023788) | software resource, software toolkit | Software R package interface between KEGG pathway and graph object as well as collection of tools to analyze, dissect and visualize these graphs. | Kyoto Encyclopedia of Genes and Genomes, KEGG, KEGG pathways, graph models, graph object, graphs visualization, | is listed by: Bioconductor | PMID:19307239 | Free, Available for download, Freely available | SCR_023788 | Kyoto Encyclopedia of Genes and Genomes graph | 2026-02-16 09:50:34 | 14 | ||||||||
|
ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | software application, software resource, standalone software | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | ReadqPCR - Read qPCR data | 2026-02-16 09:45:10 | 0 | ||||||
|
topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software resource, software toolkit | Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. | r, go, go graph, local similarities, software tool, software package, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite works with: Gene Ontology is hosted by: Bioconductor |
Available for download | biotools:topgo | https://bio.tools/topgo | SCR_014798 | 2026-02-16 09:48:40 | 2839 | ||||||||
|
BHC Resource Report Resource Website |
BHC (RRID:SCR_006399) | BHC | software application, data processing software, software resource | Software package that performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data and also includes a randomised algorithm which is more efficient for larger data sets. | clustering, microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19660130 | GNU General Public License, v3 | OMICS_02215 | SCR_006399 | Bayesian Hierarchical Clustering | 2026-02-17 10:01:06 | 0 | ||||||
|
PICS Resource Report Resource Website 1+ mentions |
PICS (RRID:SCR_001093) | software application, data processing software, data analysis software, software resource, sequence analysis software | R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach. | chip seq, bayes, data, r, sequence analysis software |
is listed by: OMICtools is hosted by: Bioconductor |
PMID:20528864 | Free, Available for download, Freely available | OMICS_00455 | SCR_001093 | Probabilistic inference of ChIP-seq | 2026-02-17 09:59:34 | 3 | |||||||
|
EnhancedVolcano Resource Report Resource Website 100+ mentions |
EnhancedVolcano (RRID:SCR_018931) | data visualization software, data processing software, software application, software resource | Software R package to produce publication ready volcano plots with enhanced colouring and labeling. Used to visualise results of differential expression analyses. | Publication ready plot, enhanced coloring, enhanced labeling, data visualisation, differential expression analyses, plot, volcano plot |
uses: ggplot2 uses: ggrepel is listed by: Bioconductor |
Free, Available for download, Freely available | https://github.com/kevinblighe/EnhancedVolcano | SCR_018931 | 2026-02-17 10:03:50 | 469 | |||||||||
|
DEGreport Resource Report Resource Website 10+ mentions |
DEGreport (RRID:SCR_018941) | data analysis software, software application, data processing software, software resource | Software R package for creation of HTML report of differential expression analyses of count data. Integrates some of code mentioned in DESeq2 and edgeR vignettes, and reports ranked list of genes according to fold changes mean and variability for each selected gene. | HTML report creation, differential expression analyses, count data, code integration, gene list report | is listed by: Bioconductor | Free, Available for download, Freely available | http://lpantano.github.io/DEGreport | SCR_018941 | 2026-02-17 10:03:10 | 16 | |||||||||
|
ReactomePA Resource Report Resource Website 50+ mentions |
ReactomePA (RRID:SCR_019316) | software application, data processing software, data analysis software, software resource, data visualization software | Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. | pathway analysis, REACTOME pathway, REACTOME database, enrichment analysis, gene set enrichment analysis, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
PMID:26661513 | Free, Available for download, Freely available | biotools:reactomepa | https://bio.tools/reactomepa | SCR_019316 | Reactome Pathway Analysis | 2026-02-17 10:03:16 | 76 | ||||||
|
MSnbase Resource Report Resource Website 10+ mentions |
MSnbase (RRID:SCR_019317) | software application, data processing software, data analytics software, software resource, software toolkit, data visualization software | Software R package provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. Used for isobaric tagged mass spectrometry data visualization, processing and quantitation. | Mass spectrometry data processing, mass spectrometry data visualization, raw mass spectrometry data | is listed by: Bioconductor | BBSRC Tools and Resources Development Fund ; European Union 7th Framework Program |
PMID:22113085 PMID:32902283 |
Free, Available for download, Freely available | SCR_019317 | 2026-02-17 10:03:55 | 10 | ||||||||
|
biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | data analysis software, software application, data processing software, software resource | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-02-17 10:03:14 | 2638 | ||||||
|
GSVA Resource Report Resource Website 100+ mentions |
GSVA (RRID:SCR_021058) | GSVA | software application, data processing software, data analysis software, software resource, software toolkit | Open source software R package for assaying variation of gene set enrichment over sample population.Used for microarray and RNA-seq data analysis. Gene set enrichment method that estimates variation of pathway activity over sample population in unsupervised manner. | Gene set enrichment, variation estimation, pathway activity, sample population, microarray, RNA-seq, data analysis | is listed by: Bioconductor | ISCIII COMBIOMED ; Spanish MINECO ; NCI U54 CA149237 |
PMID:23323831 | Free, Available for download, Freely available | SCR_021058 | Gene Set Variation Analysis | 2026-02-17 10:03:18 | 256 | ||||||
|
PhenStat Resource Report Resource Website 1+ mentions |
PhenStat (RRID:SCR_021317) | software application, data processing software, data analysis software, software resource, software toolkit | Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data. | Statistical analysis, phenotypic data, standardized analysis, bio.tools, Bioconductor |
is listed by: Bioconductor is listed by: bio.tools |
Wellcome Trust ; NHGRI U54 HG006370 |
PMID:26147094 | Free, Available for download, Freely available | biotools:phenstat | https://bio.tools/phenstat | SCR_021317 | 2026-02-17 10:04:03 | 8 |
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