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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Opal Research Resource Report Resource Website 1+ mentions |
Opal Research (RRID:SCR_000405) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software which integrates a comprehensive, automated genome annotation engine with the VAAST and Phevor disease gene prioritization tools to rank gene variants on the severity of their impact on protein function and likelihood to cause disease. Each variant in a gene is analyzed for its impact on protein function, conservation and frequency. Each gene is ranked rather than filtered in order to ensure critical targets are not prematurely removed. | sequence analysis software, genome interpretation, variant prioritization, disease gene prioritization, next-generation sequencing, clinical interpretation, clinical genomics software, genome, protein function, disease, genomic variant, mutation | is related to: VAAST | PMID:23895124 | Restricted | SciRes_000140 | SCR_000405 | Omicia Opal Research, Omicia Opal, Opal Research Variant Interpretation | 2026-09-05 06:24:18 | 1 | |||||||
|
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 | 2026-09-05 06:24:21 | 102 | ||||
|
Reprever Resource Report Resource Website |
Reprever (RRID:SCR_000463) | Reprever | software resource | Software that identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon for any genomic regions that are increased in copy number. | genomics, genomic region, insertion breakpoint, insertion, breakpoint, duplicon, genome |
is listed by: OMICtools has parent organization: SourceForge has parent organization: University of California at San Diego; California; USA |
PMID:23658221 | Free, Available for download, Freely available | OMICS_01561 | SCR_000463 | Reprever: resolving low-copy duplicated sequences using template drive | 2026-09-05 06:24:20 | 0 | ||||||
|
UCSCin Resource Report Resource Website |
UCSCin (RRID:SCR_000571) | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Beta software used to align and browse a genome. | genome | has parent organization: University of Toronto; Ontario; Canada | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144379 | SCR_000571 | 2026-09-05 06:24:22 | 0 | |||||||||
|
wANNOVAR Resource Report Resource Website 10+ mentions |
wANNOVAR (RRID:SCR_000565) | wANNOVAR | analysis service resource, data analysis service, production service resource, 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 | 2026-09-05 06:24:21 | 22 | |||||||
|
Computational Cancer Genomics Group Resource Report Resource Website 1+ mentions |
Computational Cancer Genomics Group (RRID:SCR_000772) | data analysis software, data or information resource, data processing software, database, 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 | 2026-09-05 06:24:25 | 3 | ||||||||
|
GEUVADIS Resource Report Resource Website 1+ mentions |
GEUVADIS (RRID:SCR_000684) | GEUVADIS | consortium, data or information resource, organization portal, 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 | 2026-09-05 06:24:24 | 1 | ||||||
|
EUCOMMTOOLS Resource Report Resource Website 1+ mentions |
EUCOMMTOOLS (RRID:SCR_000676) | EUCOMMTOOLS | biomaterial manufacture, material service resource, production service resource, service resource | Functional Annotation of the Mouse Genome, it will complete the International Knockout Mouse Consortium (IKMC) resource of mutations for all protein coding genes. Furthermore, it will maximize the utility of the conditional IKMC resource by generating up to 250 different, mostly inducible Cre driver mouse lines. In addition, EUCOMMTOOLS will develop novel tools to enhance the versatility of the IKMC resource. EUCOMMTOOLS vectors, mutant ES cells and mutant mice are distributed worldwide: EUCOMMTOOLS mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMMTOOLS mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Knockout-first Mutant Alleles: EUCOMMTOOLS will create 3500 C57Bl/6 conditional mutant alleles for single-exon (or otherwise previously conditionally untargeted) protein-coding mouse genes. These alleles will be made predominantly by introducing an "artificial intron", containing a standard EUCOMM promoter-driven targeting cassette, into the coding sequence of the single-exon gene. Cre Resources: EUCOMMTOOLS will engineer 500 new Cre C57Bl/6 ES cell lines by Cre knock-ins into genes with useful expression patterns. The resource will be made with inducible forms of Cre recombinase such as CreERT2. Up to 250 lines of Cre driver mice on a pure C57Bl/6N background will be generated and the Cre expression patterns documented and annotated in day P14 and P56. These mice will form a matched Cre driver resource for C57Bl/6N mice produced from conditional IKMC resources. Research, Technology and Complementary Reagents: EUCOMMTOOLS will develop novel technologies to add value, depth and flexibility to existing IKMC ES cell and mouse resources. Key areas include: * Development of novel recombinase based regulatory switches * Exploration of zinc-finger nuclease stimulated homologous recombination strategies in fertilized oocytes * Development and validation of complementary modular vector reagents which enable the construction of new useful knock-in alleles such as fluorescent and other reporters, site specific recombinases, and mutant cDNAs. These novel alleles can be constructed either by re-utilizing existing IKMC modular vector resources or directly modifying existing targeted IKMC ES cell lines by RMCE. | genome, annotation, function, mutation, protein coding gene, vector, mutant embryonic stem cell, mutant mouse strain, cre driver, cre, recombinase, c57bl/6, allele, embryonic stem cell line, c57bl/6n, knock-in |
uses: EuMMCR uses: European Mouse Mutant Archive is related to: Recombinase (cre) Activity has parent organization: International Knockout Mouse Consortium |
European Union ; FP7 ; THEME Health |
nlx_152804 | SCR_000676 | EUCOMM - Tools for Functional Annotation of the Mouse Genome, EUCOMM: Tools for Functional Annotation of the Mouse Genome | 2026-09-05 06:24:23 | 1 | |||||||
|
MEGA Resource Report Resource Website 1000+ mentions |
MEGA (RRID:SCR_000667) | MEGA, MEGA6, MEGA4, MEGA 4, MEGA 11 | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny. | comparative, analysis, DNA, protein, sequence, molecular, evolution, pattern, gene, genome, evolution, FASEB list | has parent organization: Pennsylvania State University | Burroughs-Wellcome Fund ; Japan Society for the Promotion of Science ; NHGRI HG002096; NHGRI HG006039; NIGMS R01GM126567; NIGMS R35GM139504; NSF ABI 1661218 |
DOI:10.1093/molbev/msab120 PMID:24132122 PMID:31904846 PMID:22923298 PMID:21546353 PMID:17488738 PMID:15260895 PMID:11751241 PMID:8019868 |
Free, Available for download, Freely available | SCR_023017, nlx_156838 | https://www.megasoftware.net/mega4/ | SCR_000667 | MEGA11, Molecular Evolutionary Genetics Analysis, Molecular Evolutionary Genetics Analysis 6, Molecular Evolutionary Genetics Analysis 4 | 2026-09-05 06:24:23 | 2774 | ||||
|
EMBL - Bork Group Resource Report Resource Website |
EMBL - Bork Group (RRID:SCR_000810) | EMBL - Bork Group | data or information resource, laboratory portal, organization portal, portal, service resource | The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales: * genes and proteins, * protein networks and cellular processes, and * phenotypes and environments. They require both tool development and applications. Some selected projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes. The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers. All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH. The group is partially associated with Max Delbr��ck Center for Molecular Medicine (MDC), Berlin. | computational biology, gene, protein, protein network, cellular process, phenotype, environment, gene, genome, metagenome, analysis, interaction, pathway, temporal, spatial, network, genotype, phenotype, molecular process |
has parent organization: European Molecular Biology Laboratory is parent organization of: SMART is parent organization of: SmashCommunity is parent organization of: Candidate Genes to Inherited Diseases |
European Molecular Biology Laboratory ; Max-Delbruck Center for Molecular Medicine ; European Union ; BMBF ; IBM |
nlx_149173 | SCR_000810 | Bork Group - Comparative Systems Analysis (EMBL) | 2026-09-05 06:24:27 | 0 | |||||||
|
SciRoKo Resource Report Resource Website 1+ mentions |
SciRoKo (RRID:SCR_000941) | software resource | Comparative genomics software that assists in whole genome microsatellite search and investigation. The command line version is called SciRoKoCo. The perl script DesignPrimer can be used to design PCR primer pairs for the SciRoKo output. | genomics, comparative, genome, microsatellite, analysis, investigation | is listed by: OMICtools | PMID:17463017 | Free, Available for download, Freely available | OMICS_00113 | SCR_000941 | 2026-09-05 06:24:27 | 6 | ||||||||
|
Functional Biosciences Resource Report Resource Website 1+ mentions |
Functional Biosciences (RRID:SCR_000943) | service resource | A service that provides low cost DNA sequencing. They utilize microfluidic technology. | dna, sequencing, sequence, gene, genome, microfluidic, technology | is listed by: ScienceExchange | SciEx_9422 | http://www.scienceexchange.com/facilities/functional-biosciences-inc | SCR_000943 | Functional Biosciences Inc. | 2026-09-05 06:24:27 | 2 | ||||||||
|
Genome Canada Resource Report Resource Website 10+ mentions |
Genome Canada (RRID:SCR_000966) | Genome Canada | nonprofit organization | Genome Canada is a non-profit organization that is funded by the Government of Canada. The organization funds large-scale science and technology to fuel innovation regarding genomics in multiple sectors such as health, agriculture and agri-food, forestry, fisheries and aquaculture, environment, energy and mining. They create partnerships at the program and research project levels. | genome, genomics, funding, non profit, non-profit, innovation, health, agriculture, agri-food, agri food, forestry, fisheries, aquaculture, environment, energy, mining | is related to: Structural Genomics Consortium | Available to the research community | Crossref funder ID: 100008762, nlx_151964, Wikidata: Q3123000, ISNI: 0000 0001 0352 8618, grid.440163.4 | https://ror.org/029s29983 | SCR_000966 | 2026-09-05 06:24:27 | 11 | |||||||
|
CrossMap Resource Report Resource Website 10+ mentions |
CrossMap (RRID:SCR_001173) | CrossMap | software resource | A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species. | genome, assembly |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24351709 | GNU General Public License | OMICS_02184 | SCR_001173 | 2026-09-05 06:24:30 | 19 | |||||||
|
Mouse Brain Library Resource Report Resource Website 10+ mentions |
Mouse Brain Library (RRID:SCR_001112) | MBL | atlas, data or information resource, database, image collection, portal, topical portal, video resource | Collection of high resolution images and databases of brains from many genetically characterized strains of mice with aim to systematically map and characterize genes that modulate architecture of mammalian CNS. Includes detailed information on genomes of many strains of mice. Consists of images from approximately 800 brains and numerical data from just over 8000 mice. You can search MBL by strain, age, sex, body or brain weight. Images of slide collection are available at series of resolutions. Apple's QuickTime Plugin is required to view available MBL Movies. | brain, gene, genome, strain, c57bl/6j, dba/2j, a/j, genetic variant, phenotype, hippocampus, cerebellum, striatum, olfactory bulb, thalamus, neocortex, dorsal nucleus of lateral geniculate body, central nervous system |
is related to: Videoscribbler has parent organization: University of Tennessee Health Science Center; Tennessee; USA is parent organization of: MBL Pivot Collection is parent organization of: Mouse Brain Atlases |
NIMH P20 MH62009 | PMID:10857184 PMID:15043219 |
Restricted | nif-0000-00030 | SCR_001112 | MBL - Mouse Brain Library, Mouse Brain Library, The Mouse Brain Library | 2026-09-05 06:24:29 | 24 | |||||
|
SynView Resource Report Resource Website 1+ mentions |
SynView (RRID:SCR_001106) | data analysis software, data processing software, sequence analysis software, software application, software resource | A software tool for comparative visualization of genomes. It is based in the GBrowse frameworks and integrates with the annotation features. | visualization, genome, comparison, gbrowse, sequence analysis software |
is used by: PlasmoDB is used by: ApiDB CryptoDB is listed by: OMICtools has parent organization: Generic Model Organism Database Project has parent organization: University of Georgia; Georgia; USA |
PMID:16844709 DOI:10.1093/bioinformatics/btl389 |
OMICS_00947 | SCR_001106 | 2026-09-05 06:24:29 | 1 | |||||||||
|
SparseAssembler Resource Report Resource Website 1+ mentions |
SparseAssembler (RRID:SCR_001100) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for memory-efficient genome assembly. It utilizes sparse k-mer. | genome, genomics, genome assembly, k-mer, sequence analysis software, memory |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22537038 | Free, Available for download, Freely available | OMICS_00032 | SCR_001100 | 2026-09-05 06:24:29 | 1 | ||||||||
|
JBrowse Resource Report Resource Website 10+ mentions |
JBrowse (RRID:SCR_001004) | JBrowse | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets written primarily in JavaScript. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. | genome |
is used by: Genome Resources for Yeast Chromosomes is listed by: OMICtools is listed by: Debian has parent organization: Broad Institute |
NHGRI 5R01HG004483-09 | PMID:22517427 PMID:21221095 |
GNU Lesser General Public License, Account required | OMICS_00918 | https://sources.debian.org/src/jbrowse/ | SCR_001004 | 2026-09-05 06:24:28 | 32 | |||||
|
Golden Helix GenomeBrowse Resource Report Resource Website 1+ mentions |
Golden Helix GenomeBrowse (RRID:SCR_001213) | GenomeBrowse | commercial organization, data processing software, data visualization software, software application, software resource | Software tool that delivers visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. A high performance backend is paired with an user interface to make sure that your discovery process is fluid and streamlined. | Golden Helix, variant, visualization, genome |
is listed by: OMICtools has parent organization: Golden Helix Incorporated |
Free, Available for download, Freely available | OMICS_02129 | SCR_001213 | 2026-09-05 06:24:31 | 2 | ||||||||
|
GenoViewer Resource Report Resource Website |
GenoViewer (RRID:SCR_001203) | GenoViewer | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Open source viewer / browser software for the SAM / BAM format commonly used in the assembly tasks of Next Generation Sequencing data. | next-generation sequencing, sequence, mutation, windows, linux, mac os x, genome, browser, sam, bam, fasta, gff, read error, snp, mnp, insertion, deletion | is listed by: OMICtools | PMID:22359445 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02146 | https://github.com/astrid/GenoViewer | SCR_001203 | 2026-09-05 06:24:31 | 0 |
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 NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF 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 NIF then you can log in from here to get additional features in NIF 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 NIF 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.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
