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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GERP Resource Report Resource Website 50+ mentions |
GERP (RRID:SCR_000563) | GERP | software resource | Software that identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as Rejected Substitutions. Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element. GERP estimates constraint for each alignment column; elements are identified as excess aggregations of constrained columns. A false-positive rate (which is user-settable) is calculated using "shuffled" alignments in which the order of columns is randomized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genomic, evolution, rate profiling |
is listed by: OMICtools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:15965027 PMID:21152010 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00174 | https://sources.debian.org/src/gerp++/ | SCR_000563 | Genomic Evolutionary Rate Profiling, GERP++, Genomic Evolutionary Rate Profiling: GERP, GERP2 | 2026-08-15 11:21:54 | 54 | |||||
|
EthoVision XT Resource Report Resource Website 100+ mentions |
EthoVision XT (RRID:SCR_000441) | EthoVision XT | software resource | Video tracking software that tracks and analyzes the behavior, movement, and activity of any animal. | behavior, tracking | has parent organization: Noldus | rid_000100 | SCR_000441 | 2026-08-15 11:21:44 | 368 | |||||||||
|
MuTect Resource Report Resource Website 100+ mentions |
MuTect (RRID:SCR_000559) | MuTect | software resource | Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. | next-generation sequencing, somatic mutation, tumor, normal, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Cancer | PMID:23396013 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mutect, OMICS_00087 | https://bio.tools/mutect | SCR_000559 | Mutect | 2026-08-15 11:21:46 | 102 | ||||
|
Hypothes.is Resource Report Resource Website 10+ mentions |
Hypothes.is (RRID:SCR_000430) | Hypothes.is | software resource | Non-profit organization working towards developing an open platform for the collaborative evaluation of knowledge. It will combine sentence-level critique with community peer-review to provide commentary, references, and insight on top of news, blogs, scientific articles, books, terms of service, ballot initiatives, legislation and regulations, software code and more. | annotation, evaluation, annotation standard, standard specification, peer review, ASWG |
is listed by: FORCE11 has plug in: SciBot |
Alfred P. Sloan Foundation ; Shuttleworth Foundation ; Andrew W. Mellon Foundation |
nlx_156054 | SCR_000430 | 2026-08-15 11:21:44 | 12 | ||||||||
|
MetaDrug Resource Report Resource Website 1+ mentions |
MetaDrug (RRID:SCR_000461) | MetaDrug | commercial organization | A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization | pharmacology, compound, pathway, target, metabolite, prediction, toxicity, indication, metabolism, gene, protein, analysis, drug effect | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01584 | SCR_000461 | 2026-08-15 11:21:45 | 1 | ||||||||
|
Pyrocleaner Resource Report Resource Website 1+ mentions |
Pyrocleaner (RRID:SCR_000584) | Pyrocleaner | software resource | A software module for cleaning 454 pyrosequencing reads using filters such as read duplication, length, complexity, base-pair quality and number of undetermined bases. The software also uses flowgram files of paired-end sequences to validate paired-ends files of another file. | pyrosequence, assembly, rna, dna, duplication, length, complexity, bases, flowgram, paired end | is listed by: OMICtools | PMID:21615897 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01069 | SCR_000584 | 2026-08-15 11:21:46 | 1 | |||||||
|
GeneExpressionSignature Resource Report Resource Website 1+ mentions |
GeneExpressionSignature (RRID:SCR_000455) | software resource | An R package developed for the large-scale analysis of gene expression signatures. It gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest. | software package, r, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23374109 | Free, Available for download, Freely available | OMICS_04919 | SCR_000455 | GeneExpressionSignature - Gene Expression Signature based Similarity Metric | 2026-08-15 11:21:45 | 1 | |||||||
|
RegenBase Resource Report Resource Website 1+ mentions |
RegenBase (RRID:SCR_000456) | data or information resource, portal, topical portal, project portal | Information framework and knowledge base to facilitate research about nervous system regeneration. It includes minimal information standards, an ontology that is linked to other ontologies, and a knowledge base built with a triple store and a relational database. | nervous system, regeneration, disease motility, cell motility, injury, database, ontology, information framework, knowledgebase | Spinal cord injury, Nervous system injury | PMID:27055827 | Public | nlx_156707 | http://regenbase.org/wp/ | SCR_000456 | RegenBase KnowledgeBase, RegenBase - repairing the injured nervous system, Regen Base | 2026-08-15 11:21:45 | 1 | ||||||
|
Bio-Formats Resource Report Resource Website 50+ mentions |
Bio-Formats (RRID:SCR_000450) | Bio-Formats | software toolkit, standalone software, software application, software resource, software library | Standalone software Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard. | Java library, reading microscopy image data files, writing image data, standardized format, open format, |
is listed by: FORCE11 is listed by: Debian is related to: OMERO is related to: OME-TIFF Format has parent organization: OME - Open Microscopy Environment |
Wellcome Trust | Free, Available for download, Freely available | nif-0000-30175 | http://www.force11.org/node/4810, http://www.loci.wisc.edu/software/bio-formats, https://sources.debian.org/src/libbio-formats-java/ | SCR_000450 | , BioFormats, Bio-Formats Library, The Bio-Formats Library | 2026-08-15 11:21:51 | 61 | |||||
|
wANNOVAR Resource Report Resource Website 10+ mentions |
wANNOVAR (RRID:SCR_000565) | wANNOVAR | service resource, production service resource, data analysis service, analysis service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | annotate, function, genetic variant, high-throughput sequencing, single nucleotide variant, gene, variant, allele frequency, mutation, annotation, genome, insertion, deletion |
is listed by: OMICtools is related to: ANNOVAR has parent organization: University of Southern California; Los Angeles; USA |
PMID:22717648 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00194 | SCR_000565 | 2026-08-15 11:21:46 | 22 | |||||||
|
ViReMa Resource Report Resource Website 1+ mentions |
ViReMa (RRID:SCR_000566) | ViReMa | software toolkit, data processing software, software application, data analysis software, software resource | Software Python package for detection, alignment and reporting of recombination events in Next-Generation Sequencing data. Detects and reports recombination or fusion events in virus genomes using deep sequencing datasets. | virus genomes deep sequencing datasets, detection, alignment and reporting of recombination events, Next-Generation Sequencing data, |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Scripps Research Institute |
PMID:24137010 | Free, Available for download, Freely available, | OMICS_00225 | SCR_000566 | Viral Recombination Mapper | 2026-08-15 11:21:54 | 2 | ||||||
|
Salk Institute for Biological Studies Resource Report Resource Website 1+ mentions |
Salk Institute for Biological Studies (RRID:SCR_000752) | institution | The Salk Institute conducts research within three major areas of study: Molecular Biology and Genetics; Neurosciences; and Plant Biology. Six key areas represent strategic research priorities: Chemistry and Proteomics; Stem Cell Biology; Cell Biology; Regulatory Biology; Metabolic Research; and Computational and Theoretical Biology. | organization portal, meeting resource, genetics, disease, disorder, human, metabolic research, molecular biology, neuroscience, plant biology, proteomics, regulatory biology, stem cell biology, theoretical biology |
is parent organization of: Mammalian Brain Methylomes is parent organization of: neurospy is parent organization of: Computational Neurobiology Laboratory at the Salk Institute is parent organization of: Brain Cell Methylation Viewer is parent organization of: CEMBA MethylC Seq Pipeline is parent organization of: Whole Mouse Brain Cell and Genome Atlas is parent organization of: Salk Institute Biophotonics Core Facility is parent organization of: Salk Institute Flow Cytometry Core Facility is parent organization of: Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core Facility is parent organization of: Salk Institute Mass Spectrometry Core Facility is parent organization of: Salk Institute Scientific Core Facilities Senior Director's Office is parent organization of: Salk Institute Single-Cell and Spatial Omics Core Facility is parent organization of: Salk Institute Next Generation Sequencing Core (NGS) |
Aging | March of Dimes ; Donations ; San Diego City Council |
grid.250671.7, Wikidata: Q1351061, nif-0000-10414, ISNI: 0000 0001 0662 7144 | https://ror.org/03xez1567 | SCR_000752 | Salk Institute | 2026-08-15 11:21:58 | 1 | ||||||
|
Mini Analysis Guide for Microarrays Resource Report Resource Website 1+ mentions |
Mini Analysis Guide for Microarrays (RRID:SCR_000596) | MAGMA | data or information resource, narrative resource, experimental protocol | A collection of cook-book like manuals for various microarray designs. MAGMA is a collaboration between the Norwegian Microarray Consortium NMC and MolMine AS | microarray design, microarray, manual, guide, array, analysis, j-express, import, data processing, global analysis, differential expression, gene set, co-expressed gene |
is listed by: OMICtools has parent organization: J-Express |
OMICS_00772 | SCR_000596 | 2026-08-15 11:21:46 | 3 | |||||||||
|
e-mouse.org Resource Report Resource Website 1+ mentions |
e-mouse.org (RRID:SCR_000623) | e-mouse, e mouse | data or information resource, portal, topical portal | The e-mouse.org is an online resource that aims to bring together and provide users with all information related to the laboratory mouse and its use as a model organism. Users can find direct links to MRB, a resource management project that provides a dynamic and interactive view of most world wide available mouse resources, as well as the CreZOO, MMdb and Fleming Databases, three more specialized mouse repositories, all developed and hosted at the B.S.R.C. Alexander Fleming Institute. Additionally e-mouse.org provides links to major European and international mouse resources like the Mouse Genome Informatics (MGI), European Mouse Mutant Archive (EMMA), International Mouse Strain Resource (IMSR) and Ensembl. Users interested in retrieving information regarding the use of mouse models are encouraged to visit MRB which provides an index of publicly available mouse resources intended for both bench scientists and bioinformaticians. * Mouse Resource Browser (MRB) is a resource management project that provides a dynamic and interactive view of most world wide available mouse resources, classified in 22 categories. * CreZOO is the European virtual repository of Cre and other targeted conditional driver strains. Its aim is to capture and disseminate extant and new information on all Cre driver strains. * MUGEN Mouse Database (MMdb) is a virtual and fully searchable repository of murine models of immune processes and immunological diseases. * Fleming Database is a fully searchable resource developed to host all mouse strains developed and/or housed in BSRC Al. Fleming's animal house. * MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. * EMMA is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. * IMSR is a searchable online database of mouse strains and stocks available worldwide, including inbred, mutant, and genetically engineered mice. The goal of the IMSR is to assist the international scientific community in locating and obtaining mouse resources for research. * Ensembl is a project that produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online. | model organism, database | has parent organization: BSRC Al. Fleming; East Attica; Greece | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151621 | SCR_000623 | 2026-08-15 11:21:46 | 1 | ||||||||
|
PredSL Resource Report Resource Website 1+ mentions |
PredSL (RRID:SCR_000626) | PredSL | data access protocol, software resource, web service | Web tool using an algorithm that exploits neural networks, Markov Chains, and HMMs for the prediction of the subcellular localization of proteins in eukaryotic cells from the N-terminal amino acid sequence and aims to classify proteins into five groups: Chloroplast, Thylakoid, Mitochondrion, Secreted proteins, and Other. As input PredSL requires the protein's sequence in fasta format. | subcellular localization of proteins prediction, proteins in eukaryotic cells prediction, N-terminal amino acid sequence prediction, classify proteins, | has parent organization: University of Athens Biophysics and Bioinformatics Laboratory | PMID:16689702 | nlx_151739 | http://hannibal.biol.uoa.gr/PredSL/ | SCR_000626 | PREDiction of Subcellular Location from the N-terminal Sequence | 2026-08-15 11:21:55 | 5 | ||||||
|
CorQ Resource Report Resource Website 1+ mentions |
CorQ (RRID:SCR_000660) | software resource | A set of perl programs that correct errors in 454 pyrosequences by identifying and flagging poor quality insertions, deletions and substitutions within an alignment. The algorithm utilizes the inherent base quality in sequence-specific context to correct for homopolymer and non-homopolymer insertion and deletion errors. CorQ also takes uneven read mapping into account for correcting pyrosequencing miscall errors and it identifies and corrects carry forward errors. | homopolymer, indel, corq, uneven read mapping, pyrosequence error, forward errors |
is listed by: OMICtools has parent organization: University of Washington; Seattle; USA |
PMID:24039850 | OMICS_01039 | SCR_000660 | 2026-08-15 11:21:47 | 1 | |||||||||
|
Biometric Research Branch: ArrayTools Resource Report Resource Website 1+ mentions |
Biometric Research Branch: ArrayTools (RRID:SCR_000778) | software toolkit, data processing software, software application, data analysis software, software resource, data visualization software | A software package for the visualization and statistical analysis of DNA microarray gene expression data. The tools have been developed from the R statistical system, in C and fortran programs and Java applications. They are integrated into Excel as an add-in. | visualization, statistic, analysis, dna, microarray, gene, expression, c, java, excel |
is listed by: OMICtools has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30199 | SCR_000778 | BRB ArrayTools | 2026-08-15 11:21:59 | 6 | ||||||||
|
Computational Cancer Genomics Group Resource Report Resource Website 1+ mentions |
Computational Cancer Genomics Group (RRID:SCR_000772) | database, data processing software, data or information resource, data analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Computational Cancer Genomics (CCG) group is dedicated to the development of analysis tools and databases relating molecular sequences and biological functions. Sponsors: This group is supported by the Swiss Institute of Bioinformatics (SIB). | eukaryotic, expression, function, gene, analyzer, annotation, biological, clustering, computational, data, genome, in vitro, mapping, messengerrna, molecular, mpss, mrna, one-dimensional, organism, promoter, sage, sequence, snp, software, tag, technology, tool, transcription, transcriptome | has parent organization: SIB Swiss Institute of Bioinformatics | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25561 | SCR_000772 | CCG | 2026-08-15 11:21:59 | 3 | ||||||||
|
GenomeWeb Resource Report Resource Website 1+ mentions |
GenomeWeb (RRID:SCR_000650) | GenomeWeb | video resource, blog, data or information resource, job resource, narrative resource | An independent, privately-held online and print publisher based in New York that serves the global community of scientists, technology professionals, and executives who use and develop the latest advanced tools in molecular biology research and molecular diagnostics. GenomeWeb's editorial mission is to serve readers with exclusive, in-depth coverage of the technology, institutions, and scientists that make up the worldwide research enterprise of molecular biology. We operate the largest online news organization focused on advanced research tools in genomics, proteomics, and bioinformatics. Our expert editors report and write with precision and clarity. GenomeWeb users can be found in major scientific organizations around the world, including biopharmaceutical companies, important research universities, biomedical institutes, and government laboratories. Our advertisers include leading suppliers of research tools, analytical instruments, and information technology. Getting started is easy - just register, and use your workplace e-mail address to maximize your access to content. Once you're logged in, you'll have complete free access to GenomeWeb Daily News, The Daily Scan, all of Genome Technology magazine, every GenomeWeb blog, and much more. GenomeWeb Free Content * GenomeWeb Daily News offers breaking news as well as feature articles on genomics, proteomics, bioinformatics, and more. Daily News covers not only the science and business news, but also regulatory and policy updates. Published online and twice daily by e-mail bulletin. * The Daily Scan is a roundup of the most interesting mainstream media articles, blog posts, and peer-reviewed literature relevant to genomic and proteomic scientists. Published daily online and by e-mail bulletin. * Genome Technology: GenomeWeb's magazine covers news, trends, people, and technologies in the systems biology field. It also includes Tech Guides, which feature expert troubleshooting advice on specific lab challenges, and Research Trend Digests. Published 10 times per year. Subscriptions to the print edition are free to active researchers in the US and $29 per year for non-scientists or anyone outside the US. Non-US researchers are eligible for a free subscription to the digital edition of Genome Technology. We may contact subscribers from time to time to requalify for the magazine, in compliance with our third-party readership audit. * Careers: Our Careers page includes content to help scientists in their jobs, with links to relevant external blog posts, profiles of alternative job paths, and more. Careers also includes our Job Listings board, where anyone can post job ads for free. * Cancer Minute: Updated daily and published by e-mail bulletin weekly, Cancer Minute rounds up the latest oncology peer-reviewed literature as well as news and blog posts. * Informatics Iron: This blog covers high-performance computing and the hardware side of bioinformatics, from GPUs to compute clusters and more. * The Sample: This blog focuses on a range of topics of interest to clinical labs, including the adoption of molecular tools, issues related to lab management, in-depth coverage of the major reference labs, and more. GenomeWeb Premium Content All GenomeWeb premium content provides readers with in-depth, exclusive coverage in key technology or application areas. These publications include business, technology, and research news; patent and IP information; product launches and upgrades; and hirings, promotions, and other people news. | genomics, proteomics, bioinformatics, biomedical, biopharmaceutical, genomic, molecular biology, research, rnai, scientist, technology, array, mdx, informatics, pcr, mirna, sequencing |
is used by: OncoTrack is listed by: OMICtools is parent organization of: Daily Scan |
OMICS_01731, nif-0000-10238 | SCR_000650 | GenomeWeb LLC | 2026-08-15 11:21:47 | 2 | ||||||||
|
GEUVADIS Resource Report Resource Website 1+ mentions |
GEUVADIS (RRID:SCR_000684) | GEUVADIS | organization portal, data or information resource, consortium, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. A European Medical Sequencing Consortium committed to gaining insights into the human genome and its role in health and medicine by sharing data, experience and expertise in high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genetic, variation, health, disease, medical, sequencing, high-throughput sequencing, human genome, genome, genomics, personalized medicine, genomic medicine | is listed by: OMICtools | European Union ; FP7 ; HEALTH |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01779, SCR_013706 | SCR_000684 | Genetic European Variation in Health and Disease - A European Medical Sequencing Consortium, GEUVADIS Consortium, Genetic European Variation in Health and Disease | 2026-08-15 11:21:47 | 1 |
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.
