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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
RUM Resource Report Resource Website 1+ mentions |
RUM (RRID:SCR_008818) | RUM | software resource | An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
OMICS_01249, biotools:rum | https://bio.tools/rum, https://github.com/itmat/rum/wiki | SCR_008818 | Rna seq Unified Mapper | 2026-09-19 12:51:45 | 7 | |||||||
|
QuasiRecomb Resource Report Resource Website 10+ mentions |
QuasiRecomb (RRID:SCR_008812) | QuasiRecomb | software resource | A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. | haplotype, next-generation sequencing, virus, parameter, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23383997 | OMICS_00229, biotools:quasirecomb | https://bio.tools/quasirecomb | SCR_008812 | QuasiRecomb - Probabilistic inference of viral Quasispecies | 2026-09-19 12:51:45 | 33 | ||||||
|
isva Resource Report Resource Website 1+ mentions |
isva (RRID:SCR_008772) | isva | software resource | An algorithm for feature selection in the presence of potential confounding factors. | is listed by: OMICtools | OMICS_00860 | SCR_008772 | Independent Surrogate Variable Analysis, isva: Independent Surrogate Variable Analysis | 2026-09-19 12:51:45 | 3 | |||||||||
|
svd Resource Report Resource Website |
svd (RRID:SCR_008805) | svd | software resource | Interfaces to various state-of-art SVD and eigensolvers. | is listed by: OMICtools | OMICS_00862 | SCR_008805 | 2026-09-19 12:51:45 | 0 | ||||||||||
|
XPN Resource Report Resource Website 1+ mentions |
XPN (RRID:SCR_008845) | XPN | software resource | Merging Two Gene Expression Studies via Cross Platform Normalization. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
OMICS_00863, biotools:xpn | https://bio.tools/xpn | SCR_008845 | 2026-09-19 12:51:46 | 2 | ||||||||
|
MuSiC Resource Report Resource Website 100+ mentions |
MuSiC (RRID:SCR_008792) | MuSiC | software resource | A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:22759861 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:MuSiC2, OMICS_00152 | https://bio.tools/MuSiC2, https://github.com/ding-lab/MuSiC2/blob/master/README.md | SCR_008792 | Mutational Significance In Cancer | 2026-09-19 12:51:45 | 485 | |||||
|
PeakAnalyzer Resource Report Resource Website 1+ mentions |
PeakAnalyzer (RRID:SCR_001194) | PeakAnalyzer | software resource | A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution. | genome, chip, signal peak, binding site, modification site, enrichment loci, peak region, sequence, motif, chip-seq, chip-chip, c++, java, linux, mac os x, windows, bed, gtf, annotation, r, high-throughput sequencing, chromatin binding, modification loci, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:20691053 | Free, Available for download, Freely available | biotools:peakanalyzer, OMICS_02156 | https://bio.tools/peakanalyzer | SCR_001194 | 2026-09-19 12:49:36 | 3 | ||||||
|
metahdep Resource Report Resource Website |
metahdep (RRID:SCR_001225) | metahdep | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies. | differential expression, microarray, gene expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:19648140 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:metahdep, OMICS_02121 | https://bio.tools/metahdep | SCR_001225 | metahdep - Hierarchical Dependence in Meta-Analysis | 2026-09-19 12:49:36 | 0 | |||||
|
BreakSeq Resource Report Resource Website 1+ mentions |
BreakSeq (RRID:SCR_001186) | BreakSeq | software resource | Software for scanning reads from short-read sequenced genomes against a human breakpoint library to accurately identify structural variants (SVs). The library of breakpoints at nucleotide resolution were assembled from collating and standardizing ~2,000 published structural variants (SVs). For each breakpoint, its ancestral state (through comparison to primate genomes) was inferred and its mechanism of formation (e.g., nonallelic homologous recombination, NAHR). | structural variant, breakpoint, nucleotide, fasta, gff, bowtie, genomic variation, junction mapping, insertion sequence, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:20037582 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:breakseq, OMICS_02168 | https://bio.tools/breakseq | SCR_001186 | Breakpoint Library and BreakSeq | 2026-09-19 12:49:36 | 1 | |||||
|
SLOPE Resource Report Resource Website |
SLOPE (RRID:SCR_001185) | SLOPE | software resource | Software that consists of two command-line utilities, slope_align (which finds the best split-read alignments to the reference genome) and slope_cluster (which clusters and outputs the alignments)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | c++, alignment, cluster, command-line, reference genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
PMID:20876606 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02169, biotools:slope | https://bio.tools/slope | SCR_001185 | 2026-09-19 12:49:36 | 0 | ||||||
|
categoryCompare Resource Report Resource Website 1+ mentions |
categoryCompare (RRID:SCR_001223) | categoryCompare | data analysis software, data processing software, software application, 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 | 2026-09-19 12:49:36 | 9 | ||||||
|
MergeMaid Resource Report Resource Website 1+ mentions |
MergeMaid (RRID:SCR_001221) | MergeMaid | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. R extension whose functions are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be "list", "matrix", or "ExpressionSet". The main function is "mergeExprs" which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function "intcor" calculate the correlation coefficients. Other functions use the output from "modelOutcome" to graphically display the results and cross-validate associations of gene expression data with survival. | differential expression, microarray, visualization, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16646808 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02124 | SCR_001221 | Merge Maid | 2026-09-19 12:49:36 | 3 | ||||||
|
CATCHprofiles Resource Report Resource Website |
CATCHprofiles (RRID:SCR_001182) | CATCHprofiles | software resource | Software tool for exploring patterns in Chromatin Immuno Precipitation (ChIP) profiling data. The CATCH algorithm performs a hierachical clustering of the profile patterns with an exhaustive alignment at each step. The algorithm has a user-friendly graphical interface that makes it easy to browse results. | cluster, chip, alignment, chip profile |
is listed by: OMICtools has parent organization: Radboud University; Nijmegen; The Netherlands |
PMID:22238575 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02171 | SCR_001182 | CATCH - Unsupervised clustering of ChIP profiles | 2026-09-19 12:49:37 | 0 | ||||||
|
Breakway Resource Report Resource Website |
Breakway (RRID:SCR_001180) | Breakway | software resource | A suite of software programs that take aligned genomic data and report structural variation breakpoints. Features include: * Takes in BAM formatted input, the current standard for genomic alignments. * Compatible with standard output from major alignment algorithms such as BFAST, BWA, MAQ, et cetera. * Capable of analyzing data from any major platform--Solexa, SOLiD, 454, et cetera. * Empirically identifies structural variation breakpoints. * Highly specific analysis generates very few false positives. * Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives. | genome, structural variation, breakpoint |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at Los Angeles; California; USA |
PMID:20126413 | Free, Available for download, Freely available | OMICS_02176 | SCR_001180 | Breakway: Identify Structural Variations in Genomic Data | 2026-09-19 12:49:35 | 0 | ||||||
|
Genometa Resource Report Resource Website |
Genometa (RRID:SCR_001181) | Genometa | software resource | A Java based bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence. The approach is based upon the established open source visualisation tool IGB and supported by the rapid alignment program bowtie. The Picard toolset for SAM files is also made use of. | metagenomic, classify, windows, linux, java, bio.tools, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Hannover Medical School; Lower Saxony; Germany |
PMID:22927906 | Free, Available for download, Freely available | biotools:genometa, OMICS_02175 | https://bio.tools/genometa | SCR_001181 | Genometa - Rapid analysis of metagenomic short reads | 2026-09-19 12:49:36 | 0 | |||||
|
MADAM Resource Report Resource Website |
MADAM (RRID:SCR_001216) | MADAM | data management software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Data management software implemented in Java that facilitates the entry of data into a relational database. It guides users through the microarray process from RNA procurement to data analysis, offering intelligent forms to simplify the tracking of experimental parameters and results that are essential for the interpretation of expression results in downstream analyses. Canned reports provide information on RNA samples, studies, slide maps and other pertinent data and a general SQL query window allows freeform access to the underlying database. MADAM also serves as a platform for launching other data entry and management tools. Through the use of these integrated modules, users can view and score PCR plates, design experiments and studies, and track laboratory materials. | microarray, data management software, rna |
is listed by: OMICtools is related to: MicroArray and Gene Expression Markup Language has parent organization: TM4 |
PMID:20193058 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02127 | SCR_001216 | MADAM (TM4 Microarray Software Suite), TM4 Microarray Software Suite: MicroArray DAta Manager, MADAM: MicroArray DAta Manager, TM4 Microarray Software Suite: MADAM, MicroArray DAta Manager, TM4 MADAM | 2026-09-19 12:49:36 | 0 | ||||||
|
Microarray Data Analysis System Resource Report Resource Website 1+ mentions |
Microarray Data Analysis System (RRID:SCR_001218) | MIDAS | software resource | Application that provides users an interface to design analysis protocols combining one or more normalization and filtering steps. In this way, data from many individual hybridizations can be treated in a uniform and reproducible manner. | microarray, normalization, windows, mac osx, linux, java |
is listed by: OMICtools has parent organization: TM4 |
Artistic License | OMICS_02126 | https://sourceforge.net/projects/midas-tm4/ | http://www.tm4.org/midas.html | SCR_001218 | TM4 Microarray Software Suite: Microarray Data Analysis System, TM4 Microarray Software Suite: MIDAS, MIDAS (TM4 Microarray Software Suite), TM4 MIDAS, MIDAS: Microarray Data Analysis System | 2026-09-19 12:49:37 | 4 | |||||
|
globaltest Resource Report Resource Website 10+ mentions |
globaltest (RRID:SCR_001256) | globaltest | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | 2026-09-19 12:49:37 | 31 | ||||||
|
iterativeBMAsurv Resource Report Resource Website |
iterativeBMAsurv (RRID:SCR_001254) | iterativeBMAsurv | software resource | Software package providing a variable selection method for applying survival analysis to microarray data. | microarray |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19245714 | GNU General Public License, v2 or newer | OMICS_02086 | SCR_001254 | The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis, iterativeBMAsurv - The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis | 2026-09-19 12:49:37 | 0 | ||||||
|
snpStats: SnpMatrix and XSnpMatrix classes and methods Resource Report Resource Website 50+ mentions |
snpStats: SnpMatrix and XSnpMatrix classes and methods (RRID:SCR_001249) | snpStats | software resource | Software for classes and statistical methods for large single nucleotide polymorphism (SNP) association studies. | r, single nucleotide polymorphism, genetic variability, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:16720584 | Free, Available for download, Freely available | OMICS_02091 | SCR_001249 | 2026-09-19 12:49:37 | 79 |
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