Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
aCGHtool Resource Report Resource Website 1+ mentions |
aCGHtool (RRID:SCR_010915) | aCGHtool | software resource | A software tool for the normalization, visualization, breakpoint detection, and comparative analysis of array-CGH data which allows the accurate and sensitive detection of CNAs. | is listed by: OMICtools | OMICS_00699 | SCR_010915 | 2026-09-19 12:52:02 | 1 | ||||||||||
|
Agilent Genomic Workbench Resource Report Resource Website 100+ mentions |
Agilent Genomic Workbench (RRID:SCR_010918) | Agilent Genomic Workbench | software resource | A comprehensive design and analysis tool for setting up and interpreting your microarray experiments. | is listed by: OMICtools | OMICS_00702 | SCR_010918 | 2026-09-19 12:52:02 | 250 | ||||||||||
|
DBChIP Resource Report Resource Website 1+ mentions |
DBChIP (RRID:SCR_010872) | DBChIP | software resource | Detects differential binding of transcription factors with ChIP-seq. | is listed by: OMICtools | OMICS_00470 | SCR_010872 | 2026-09-19 12:52:01 | 5 | ||||||||||
|
DIME Resource Report Resource Website 10+ mentions |
DIME (RRID:SCR_010874) | DIME | software resource | R-package for identifying differential ChIP-seq based on an ensemble of mixture models. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:DIME, OMICS_00473 | https://bio.tools/DIME | SCR_010874 | 2026-09-19 12:52:01 | 31 | ||||||||
|
ChIPModule Resource Report Resource Website 1+ mentions |
ChIPModule (RRID:SCR_010877) | ChIPModule | software resource | A software tool for systematic discovery of transcription factors and their cofactors from ChIP-seq data. | is listed by: OMICtools | OMICS_00477 | SCR_010877 | ChIPModule: Systematic discovery of transcription factors and their cofactors from ChIP-seq data | 2026-09-19 12:52:01 | 1 | |||||||||
|
BWA Resource Report Resource Website 1000+ mentions |
BWA (RRID:SCR_010910) | BWA | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp. | sequence, alignment, reference, genome, human, short, long, read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill is related to: Proovread is related to: BWA-MEM2 has parent organization: SourceForge is required by: RelocaTE |
PMID:19451168 PMID:20080505 DOI:10.1093/bioinformatics/btp324 |
Free, Available for download, Freely available | SCR_015853, biotools:bwa-sw, OMICS_00654 | https://sourceforge.net/projects/bio-bwa/files/, https://bio.tools/bwa-sw, https://sources.debian.org/src/bwa/ | SCR_010910 | Burrows-Wheeler Aligner (BWA), Burrows-Wheeler Aligner | 2026-09-19 12:52:02 | 2638 | |||||
|
CloudBurst Resource Report Resource Website |
CloudBurst (RRID:SCR_010911) | CloudBurst | software resource | A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19357099 | Free | OMICS_00657, biotools:cloudburst | https://bio.tools/cloudburst | SCR_010911 | 2026-09-19 12:52:02 | 0 | ||||||
|
ERNE Resource Report Resource Website 10+ mentions |
ERNE (RRID:SCR_010912) | ERNE | software resource | A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00662 | SCR_010912 | 2026-09-19 12:52:02 | 48 | ||||||||||
|
F-Seq Resource Report Resource Website 50+ mentions |
F-Seq (RRID:SCR_010880) | F-Seq | software resource | A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser. |
is listed by: OMICtools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
OMICS_00482 | SCR_010880 | 2026-09-19 12:52:01 | 84 | ||||||||||
|
HOMER Resource Report Resource Website 5000+ mentions |
HOMER (RRID:SCR_010881) | HOMER | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++. | motif, discovery, next, generation, sequencing, analysis, genomic, data |
is listed by: OMICtools is related to: findMotif.pl has parent organization: University of California at San Diego; California; USA |
Foundation Leducq Transatlantic Network Grant ; NCI CA52599; NIDDK DK063491; NIGMS P50 GM081892; NIH HC088093; NURSA consortium grant |
PMID:20513432 | OMICS_00483 | http://biowhat.ucsd.edu/homer/index.html | SCR_010881 | HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 | 2026-09-19 12:52:01 | 5929 | |||||
|
PALMapper Resource Report Resource Website 1+ mentions |
PALMapper (RRID:SCR_011466) | PALMapper | software resource | Computes both spliced and unspliced alignments at high accuracy while taking advantage of base quality information and splice site predictions. | is listed by: OMICtools | OMICS_01245 | SCR_011466 | 2026-09-19 12:52:13 | 4 | ||||||||||
|
ExiMiR Resource Report Resource Website 1+ mentions |
ExiMiR (RRID:SCR_012753) | ExiMiR | software resource | R functions for the normalization of Exiqon miRNA array data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00783 | SCR_012753 | 2026-09-19 12:52:32 | 1 | ||||||||||
|
CNV Workshop Resource Report Resource Website 1+ mentions |
CNV Workshop (RRID:SCR_012635) | CNV Workshop | software resource | Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV). |
is listed by: OMICtools has parent organization: SourceForge |
GNU Affero General Public License | OMICS_00715 | SCR_012635 | 2026-09-19 12:52:31 | 1 | |||||||||
|
motifRG Resource Report Resource Website 1+ mentions |
motifRG (RRID:SCR_012602) | motifRG | software resource | Software tools for discriminative motif discovery using regression methods. |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24162561 | Free | OMICS_00487 | SCR_012602 | motifRG - A package for discriminative motif discovery designed for high throughput sequencing dataset | 2026-09-19 12:52:30 | 5 | |||||||
|
MiRaGE Resource Report Resource Website 10+ mentions |
MiRaGE (RRID:SCR_012738) | MiRaGE | software resource | Software package that contains functions for inference of target gene regulation by miRNA, based on only target gene expression profile. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00785 | SCR_012738 | 2026-09-19 12:52:31 | 33 | ||||||||||
|
DEXSeq Resource Report Resource Website 500+ mentions |
DEXSeq (RRID:SCR_012823) | DEXSeq | software resource | Software package focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
OMICS_01329, biotools:dexseq | https://bio.tools/dexseq | SCR_012823 | 2026-09-19 12:52:33 | 540 | ||||||||
|
CexoR Resource Report Resource Website |
CexoR (RRID:SCR_012769) | CexoR | software resource | Software for strand specific peak-pair calling in ChIP-exo replicates. |
is listed by: OMICtools has parent organization: Bioconductor |
MIT License | OMICS_00519 | SCR_012769 | CexoR: An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates | 2026-09-19 12:52:32 | 0 | ||||||||
|
edgeR Resource Report Resource Website 10000+ mentions |
edgeR (RRID:SCR_012802) | edgeR | data analysis software, data processing software, software application, software resource | Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication. | empirical, analysis, digital, gene, expression, data, R, RNA-seq data, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SARTools is related to: Bioconductor works with: tximport |
Harris and IBS Honours scholarships ; Independent Research Institutes Infrastructure Support Scheme 361646; Melbourne International Research Scholarship ; NHMRC 406657; Victorian State Government OIS grant |
PMID:19910308 DOI:10.1093/bioinformatics/btp616 |
Free, Available for download, Freely available | OMICS_01308, biotools:edger | https://bio.tools/edger, https://sources.debian.org/src/r-bioc-edger/ | SCR_012802 | edgeR, empirical analysis of digital gene expression data in R, Empirical analysis of Digital Gene Expression data in R | 2026-09-19 12:52:32 | 23868 | ||||
|
MotifLab Resource Report Resource Website 1+ mentions |
MotifLab (RRID:SCR_012649) | MotifLab | software resource | Software for a general workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. |
is listed by: OMICtools has parent organization: Norwegian University of Science and Technology; Trondheim; Norway |
Research Council of Norway | PMID:23323883 | Acknowledgement requested, Free, Public | OMICS_00486 | SCR_012649 | 2026-09-19 12:52:31 | 2 | |||||||
|
KEGG Resource Report Resource Website 10000+ mentions |
KEGG (RRID:SCR_012773) | KEGG | analysis service resource, data access protocol, data analysis service, data or information resource, database, portal, production service resource, service resource, software resource, topical portal, web service | Integrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies. | model, pathway, functional hierarchy, module, cancer, disease, drug, drug classification, orthology, ortholog, genome, gene, protein, compound, classification, biochemical reaction, pathway, ligand, biosynthesis, pathway prediction, sequence, chemical structure, human, enzyme, database, molecular interaction, metabolism, metabolomics, cellular process, structure, drug development, reaction, cell |
is used by: NIF Data Federation is used by: Arabidopsis Reactome is used by: LIPID MAPS Proteome Database is used by: globaltest is used by: MitoMiner is used by: Database for Annotation Visualization and Integrated Discovery is used by: Biochemical Pathways Reaction Kinetics Database is used by: Ultimate Rough Aggregation of Metabolic Map is used by: GEMINI is used by: In vivo - In silico Metabolite Database is listed by: 3DVC is listed by: OMICtools is affiliated with: Kyoto Encyclopedia of Genes and Genomes Expression Database is related to: PathCase Pathways Database System is related to: ExplorEnz is related to: NCBI BioSystems Database is related to: Allen Institute Neurowiki is related to: eQuilibrator is related to: GeneTrail is related to: KegTools is related to: PRODORIC is related to: hiPathDB - human integrated Pathway DB with facile visualization is related to: METLIN is related to: Kidney and Urinary Pathway Knowledge Base is related to: DAVID is related to: ConsensusPathDB is related to: ENZYME is related to: FlyMine is related to: Babelomics is related to: SynSysNet is related to: Cotton EST Database is related to: Integrated Molecular Interaction Database is related to: SEGS is related to: INMEX is related to: BioExtract is related to: ClueGO is related to: MalaCards is related to: TrED is related to: FunTree is related to: MOPED - Model Organism Protein Expression Database is related to: ProOpDB is related to: KOBAS is related to: GeneTerm Linker is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit is related to: GeneCodis is related to: FunNet - Transcriptional Networks Analysis is related to: LegumeIP is related to: Algal Functional Annotation Tool is related to: aGEM is related to: DINIES is related to: KEGG PATHWAY Database is related to: ShinyGO is related to: KEGGREST has parent organization: Kyoto University; Kyoto; Japan has parent organization: University of Tokyo; Tokyo; Japan is parent organization of: KegTools works with: DIANA-mirPath works with: MiMeDB |
Japan Science and Technology Agency ; Japanese Ministry of Education Culture Sports Science and Technology MEXT |
PMID:22700311 PMID:22130871 PMID:22080510 PMID:19880382 PMID:19172790 PMID:18428742 PMID:18287706 PMID:18077471 PMID:16381885 PMID:16014746 PMID:14681412 PMID:12539951 PMID:11752249 PMID:10928937 PMID:10592173 PMID:9847135 |
Restricted | nlx_31015, OMICS_01583, OMICS_03010, OMICS_01582, OMICS_03974, OMICS_05434, OMICS_05360 | http://www.genome.jp/kegg/ | SCR_012773 | KEGG - Kyoto Encyclopedia of Genes and Genomes, Kyoto Encyclopedia of Genes and Genomes | 2026-09-19 12:52:32 | 81488 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
