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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MxPro QPCR Resource Report Resource Website 500+ mentions |
MxPro QPCR (RRID:SCR_016375) | data analysis software, data processing software, software application, software resource | Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pcr, qpcr, polymerase, qualitative, analysis, nucleic, acid, gene | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016375 | MxPro QPCR Software | 2026-09-05 06:28:07 | 543 | ||||||||||
|
findMotif.pl Resource Report Resource Website 1+ mentions |
findMotif.pl (RRID:SCR_016417) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software tool to analyze the promoters of genes and look for motifs that are enriched in the target gene promoters relative to other promoters. Used for gene based analysis to provide a list of genes that should contain the same elements, such as genes that are co-regulated. It includes gene ontology analysis and can be used to look for RNA motifs in mRNAs. | analyze, promoter, gene, motif, target, relative, same, element, ontology, RNA, mRNA |
is related to: HOMER has parent organization: University of California at San Diego; California; USA |
Free, Available for download, Freely available | SCR_016417 | 2026-09-05 06:28:08 | 4 | ||||||||||
|
SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | data analysis software, data processing software, software application, software resource, software toolkit | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-09-05 06:28:07 | 2 | |||||
|
Tests for deviation from Hardy-Weinberg equilibrium Resource Report Resource Website 10+ mentions |
Tests for deviation from Hardy-Weinberg equilibrium (RRID:SCR_016496) | data analysis software, data processing software, software application, software resource | Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases. | deviation, Hardy-Weinberg, equilibrium, test, association, population, genetic, identify, susceptibility, gene, disease, single, nucleotide, polymorphisms, snp, allele | SCR_016496 | 2026-09-05 06:28:09 | 18 | ||||||||||||
|
Drug Gene Budger Resource Report Resource Website |
Drug Gene Budger (RRID:SCR_016489) | DGB | data access protocol, service resource, software resource, web service | Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures. | identify, drug, small, molecule, predict, influence, expression, mammalian, gene, regulate, target |
is related to: LINCS Project has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA works with: CMAP works with: Gene Expression Omnibus (GEO) |
BD2K-LINCS Data Coordination and Integration Center Mount Sinai Knowledge Management Center for IDG ; NCI U24 CA224260; NHLBI U54 HL127624 |
PMID:30169739 | Restricted | SCR_016489 | Drug Gene Budger | 2026-09-05 06:28:09 | 0 | ||||||
|
Thermo Fisher: GeneChip� Scanner 3000 7G Resource Report Resource Website 1+ mentions |
Thermo Fisher: GeneChip� Scanner 3000 7G (RRID:SCR_016522) | instrument resource | Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis. | Instrument, microarray, analysis, scan, next, generation, array, whole, genome, gene, chip | Commercially available | https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk, https://drive.google.com/file/d/1du6GBtNmdw3AWBFSjRx9YQMzbZWj4uAY/view?usp=drivesdk | https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FGSD%2FDatasheets%2Fgenechip_scanner_3000_datasheet.pdf | SCR_016522 | 2026-09-05 06:28:10 | 1 | |||||||||
|
SABRe CVD Initiative Resource Report Resource Website |
SABRe CVD Initiative (RRID:SCR_016572) | SABRe CVD | data or information resource, disease-related portal, portal, topical portal | Project to generate extensive biomarker data from Framingham Heart Study participants using immunoassays, proteomics, metabolomics/lipomics, and gene expression and microRNA profiling to advance personalized medicine through biomarker discovery and validation. | generate, biomarker, discovery, data, Framingham, Heart, Study, gene, expression, omicdata | cardiovascular disease, atherosclerosis | Free, Partially available for public, Requested authorized access | SCR_016572 | Systems Approach to Biomarker Research in CardioVascular Disease | 2026-09-05 06:28:11 | 0 | ||||||||
|
MentaLiST Resource Report Resource Website 10+ mentions |
MentaLiST (RRID:SCR_016469) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome BC ; Genome Canada |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2026-09-05 06:28:09 | 15 | ||||||
|
babelgene Resource Report Resource Website 1+ mentions |
babelgene (RRID:SCR_027117) | software resource, software toolkit | Software R package to convert between human and non-human gene orthologs/homologs. Integrates orthology assertion predictions sourced from multiple databases as compiled by the HGNC Comparison of Orthology Predictions (HCOP) (Wright et al. 2005 , Eyre et al. 2007 , Seal et al. 2011 ). | Integrate orthology assertion predictions, convert, gene, orthologs, homologs | Free, Available for download, Freely available | SCR_027117 | 2026-09-05 06:35:39 | 1 | |||||||||||
|
University of South Carolina Functional Genomics Core Facility Resource Report Resource Website |
University of South Carolina Functional Genomics Core Facility (RRID:SCR_026178) | FGC | access service resource, core facility, service resource | Core offers resources and solutions for conducting genomics, transcriptomics, epigenomics and functional genomics projects. We work with researchers to determine project goals and design custom solutions. We assist at all stages of the project, from support in grant development to generation of publication-quality data. Services include Consultations, Bioinformatics, Nucleic Acids purification, quantification and QC DNA Sequencing (SANGER and NGS), Library Constructions for NGS applications,Microarray Hybridization, Real Time PCR, Custom epigenomics applications, Lentiviral vectors and lentiviruses construction and production, CRIPR-CAS9sgRNAs and RNAi/shRNAs knockdown of individual genes and functional screening of sgRNA and shRNA libraries for target identification. | gene, bioinformatics, DNA, PCR, genomics, transcriptomics, epigenomics, functional genomics, services |
is listed by: ABRF CoreMarketplace is related to: University of South Carolina Instrumentation Resource Core Facility has parent organization: University of South Carolina; South Carolina; USA |
ABRF_2990 | https://coremarketplace.org/?FacilityID=2990&citation=1, https://sc.ilab.agilent.com/service_center/show_external/6263/functional_genomics_core | SCR_026178 | University of South Carolina Functional Genomics Core | 2026-09-05 06:35:15 | 0 | |||||||
|
pfSNP Resource Report Resource Website 1+ mentions |
pfSNP (RRID:SCR_002167) | pfSNP | data or information resource, data repository, database, service resource, storage service resource | Search engine integrating various bio-informatic resources and algorithims to produce a one-stop resource for biologists to identify potentially functional SNPs. It caters to different groups of scientists interested in SNPs including those working in the following areas: * Whole-genome association studies * Gene-based association studies * Designing experiments to address the functionality of specific SNPs * Determining potentially functionally significant SNPs that are in LD with non-pfSNPs of interest. Users may add published SNP functions. | single nucleotide polymorphism, function, association study, gene, genome |
is listed by: OMICtools has parent organization: National University of Singapore; Singapore; Singapore |
PMID:20672376 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01854 | SCR_002167 | Potentially Functional SNP Search Engine, pfSNP Search Engine | 2026-09-05 06:24:44 | 7 | ||||||
|
Autosomal Recessive Polycystic Kidney Disease Mutation Database Resource Report Resource Website 10+ mentions |
Autosomal Recessive Polycystic Kidney Disease Mutation Database (RRID:SCR_002290) | data or information resource, data repository, database, service resource, storage service resource | Catalog of all changes detected in PKHD1 (Polycystic Kidney and Hepatic Disease 1) in a locus specific database. Investigators are invited to submit their novel data to this database. These data should be meaningful for clinical practice as well as of relevance for the reader interested in molecular aspects of polycystic kidney disease (PKD). There are also some links and information for ARPKD patients and their parents. Autosomal recessive polycystic kidney disease (ARPKD/PKHD1) is an important cause of renal-related and liver-related morbidity and mortality in childhood. This study reports mutation screening in 90 ARPKD patients and identifies mutations in 110 alleles making up a detection rate of 61%. Thirty-four of the detected mutations have not been reported previously. Two underlying mutations in 40 patients and one mutation in 30 cases are disclosed, and no mutation was detected on the remaining chromosomes. Mutations were found to be scattered throughout the gene without evidence of clustering at specific sites. PKHD1 mutation analysis is a powerful tool to establish the molecular cause of ARPKD in a given family. Direct identification of mutations allows an unequivocal diagnosis and accurate genetic counseling even in families displaying diagnostic challenges. | clinical, gene, genetic, mutation, protein, recessive, renal | has parent organization: RWTH Aachen University; Aachen; Germany | Autosomal recessive polycystic kidney disease, Polycystic kidney disease | PMID:16199545 PMID:11919560 |
Permission required, Terms of use | nif-0000-21038 | http://www.humgen.rwth-aachen.de/index.asp?subform=database.html&nav=database_nav.html | SCR_002290 | Mutation Database Autosomal Recessive Polycystic Kidney Disease (ARPKD/PKHD1) | 2026-09-05 06:24:46 | 14 | |||||
|
JGI Genome Portal Resource Report Resource Website 500+ mentions |
JGI Genome Portal (RRID:SCR_002383) | data or information resource, department portal, organization portal, portal | Portal providing access to all JGI genomic databases and analytical tools, sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. | gene, computation, genome, genomics, model organism, assembly, annotation, sequenced genome, metagenome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: DOE Joint Genome Institute is parent organization of: Takifugu rubripes Genome |
Department of Energy | PMID:24225321 PMID:22110030 |
nif-0000-21230, SCR_004706, OMICS_01654, biotools:jgi_genome_portal, nlx_69965 | http://genome.jgi-psf.org, https://bio.tools/jgi_genome_portal | http://genome.jgi-psf.org/ | SCR_002383 | JGI Genome Portal, DOE Joint Genome Institute Genome Portal | 2026-09-05 06:24:47 | 869 | |||||
|
Genevestigator Resource Report Resource Website 100+ mentions |
Genevestigator (RRID:SCR_002358) | Genevestigator | analysis service resource, commercial organization, data analysis service, data or information resource, database, production service resource, service resource | A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools. | gene, genetic, animal, development, disease, meta-analysis, regulation, stage, microarray, rnaseq, visualization, gene expression, disease, drug, tissue, cancer, genotype, pharma, biomedical, conditions, genotype, anatomy, neoplasm, chemical, hormone, infection, model organism, organ, cell type, cell line, target, biomarker, similarity, FASEB list | is parent organization of: RefGenes | 4 products:, Free, Free for academic use, Account required, Paid subscription, Local installation | nif-0000-21172, OMICS_00763 | SCR_002358 | 2026-09-05 06:24:47 | 407 | ||||||||
|
Centre for Modeling Human Disease Gene Trap Resource Resource Report Resource Website 1+ mentions |
Centre for Modeling Human Disease Gene Trap Resource (RRID:SCR_002785) | CMHD Gene Trap Resource | biomaterial manufacture, material service resource, production service resource, service resource | Generate gene trap insertions using mutagenic polyA trap vectors, followed by sequence tagging to develop a library of mutagenized ES cells freely available to the scientific community. This library is searchable by sequence or key word searches including gene name or symbol, chromosome location, or Gene Ontology (GO) terms. In addition,they offer a custom email alert service in which researchers are able to submit search criteria. Researchers will receive automated e-mail notification of matching gene trap clones as they are entered into the library and database. The resource features the use of complementary second and third generation polyA trap vectors developed by the Stanford lab and the laboratory of Professor Yasumasa Ishida of the Nara Institute of Science and Technology (NAIST) in Japan to mutagenize murine embryonic stem (ES) cells. CMHD gene trap clones are distributed by the Canadian Mouse Mutant Repository(CMMR). Information about ordering, services, and pricing can be found on their web site (http://www.cmmr.ca/services/index.html)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | embryonic stem cell, polya trap vector, gene trap, insertion, mutagenic polya trap vector, sequence, expression, mutagenesis, gene, mutation, expression profile, phenotype, database, gene expression, vector insertion, expressed sequence tag, blast, clone |
is related to: Gene Ontology is related to: CMMR - Canadian Mouse Mutant Repository is related to: International Gene Trap Consortium has parent organization: CMHD - Centre for Modeling Human Disease |
Canadian Institutes of Health Research ; Genome Canada ; Genome Prairie ; NIH |
PMID:14681480 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02891 | http://www.cmhd.ca/sub/genetrap.asp | SCR_002785 | Centre for Modeling Human Disease (CMHD) Gene Trap Resource | 2026-09-05 06:24:53 | 3 | ||||
|
Reflect Resource Report Resource Website 50+ mentions |
Reflect (RRID:SCR_002714) | Reflect | data access protocol, software application, software resource, web service | Web service that tags gene, protein, and small molecule names in any web page. Clicking on a tagged term opens a small popup showing summary information, and allows the user to quickly link to more detailed information. For each protein or gene, Reflect provides domain structure, sub-cellular localization, 3D structure, and interaction partners. For small molecules, it provides the chemical structure and interaction partners. Reflect can be installed as a plugin to Firefox or Internet Explorer, or can be used by entering a URL in the field provided. It can also be accessed programmatically via a REST or SOAP API, and a Reflect button can easily be added to any web page using Javascript or using a CGI proxy. Reflect was first-prize winner out of over 70 submissions in the Elsevier Grand Challenge, an international competition for systems that improve the way scientific information is communicated and used. Reflect can be edited and improved by the community. | text mining, semantic mark up, gene, protein, computational linguistics, small molecule, domain structure, sub-cellular localization, 3d structure, interaction, chemical structure |
is listed by: OMICtools is listed by: FORCE11 has parent organization: University of Copenhagen; Copenhagen; Denmark has parent organization: European Bioinformatics Institute |
PMID:19513049 | nif-0000-23349, OMICS_01196 | http://reflect.ws/ | SCR_002714 | Reflect: Protein small molecules | 2026-09-05 06:24:52 | 88 | ||||||
|
Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis Resource Report Resource Website 50+ mentions |
Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (RRID:SCR_002676) | CAMERA | analysis service resource, data analysis service, data or information resource, data repository, organization portal, portal, production service resource, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data. | ecology, energy, environment, gene, analysis, bioinformatics, biological, biology, community, cyberinfrastructure, data, dna, genome, genomics, health care, map, marine, metadata, metagenomic, microbial, microbiology, molecular biology, organism, research, scientific, sequence, sequencing, software, tool, training, viral |
is listed by: OMICtools is related to: VIROME has parent organization: University of California at San Diego; California; USA |
Gordon and Betty Moore Foundation | PMID:21045053 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_011924, OMICS_01476, nif-0000-23292 | SCR_002676 | 2026-09-05 06:24:51 | 83 | ||||||
|
Genes to Cognition Online Resource Report Resource Website 1+ mentions |
Genes to Cognition Online (RRID:SCR_002746) | G2C | blog, data or information resource, narrative resource, portal, software application, software resource, topical portal, training material | Genes to Cognition (G2C) Online is about modern neuroscience. It focuses on cognitive disorders, cognitive processes, and research approaches. Use the dynamic network maps to explore our library of 750+ unique items. Or, use the linear Selected Items menu on top of each map to tour selected content. Read the G2C blog, use simple mapper, or the 3-D brain, an interactive model of the brain. Disorders included in this site: ADHD, Alzheimer's Disease, Autism, Bipolar Disorder, Depression, Schizophrenia Cognitive Processes include: Attention, Language, Learning and Memory, Perception, and Thinking Research Approaches include: Bioinformatics, Ethics, Gene Finding, Model systems, Neuroimaging, Psychology. Navigation: Interact with the dynamic Networks Maps to explore the full catalog of content. Roll-over a node on the map for a preview and click to open the content. Move on to other content by returning to the network map. Each node you visit on the map gets flagged. Follow the Selected Items Subway Line for an overview of a topic. Roll-over a subway node for a preview and click to open the content. Other Features: Most content items include links to Related Items, which allow you to explore further. The Glossary includes over 300 neuroscience keywords. Search for content using keywords or id number. Select a preferred network map to view the content in context. Open/close the History at the lower left to view visited content. Your history is stored until you clear it. Simple Mapper - We developed Simple Mapper to power this web site on the brain. Now, you can use it to organize what comes out of yours! With Simple Mapper create and save concept maps, network diagrams, or flowcharts for personal use or to share with others. 3-D Brain - The G2C Brain is an interactive 3-D model of the brain, with 29 structures that can be rotated in three-dimensional space. Each structure has information on brain disorders, brain damage, case studies, and links to modern neuroscience research. Ideal for students, researchers, and educators in psychology and biology. Also available for download: 3D Brain App for iPhone and iPod Touch! | gene, cognition, cognitive, disorder, map, network, neuroscience, process, research, biochemical, cell, brain anatomy, environment, k-12 |
is related to: 3D Brain has parent organization: Cold Spring Harbor Laboratory |
The Dana Foundation ; William and Flora Hewlett Foundation |
Free, Freely available | nif-0000-25051 | SCR_002746 | G2C Online | 2026-09-05 06:24:53 | 6 | ||||||
|
Sherlock Resource Report Resource Website 50+ mentions |
Sherlock (RRID:SCR_001628) | Sherlock | data or information resource, service resource | Service to discover disease genes in GWAS using eQTL signature matching by simply submitting your list of GWAS associations (SNPs and p-values). It is important to upload all SNPs in your association study, not just the top hits. Sherlock may be able to group multiple lower-confidence SNPs to discover functionally-important genes. | genome-wide association study, expression quantitative trait locus, disease gene, snp, gene expression, gene, disease, association, p-value, cis, trans, genetic variation, mapping, phenotype, FASEB list | has parent organization: University of California at San Francisco; California; USA | NIGMS R01GM070808; NIGMS U19GM61390; NIGMS P50 GM081879 |
PMID:23643380 | Free, Freely available | nlx_153895 | SCR_001628 | 2026-09-05 06:24:36 | 90 | ||||||
|
rSeqDiff Resource Report Resource Website |
rSeqDiff (RRID:SCR_001683) | rSeqDiff | software resource | An R package that can detect differential gene and isoform expressions from RNA-seq data of multiple biological conditions. The approach considers three cases for each gene: 1) no differential expression, 2) differential expression without differential splicing and 3) differential splicing. | rna-seq, gene expression, differential expression, differential splicing, gene |
is listed by: OMICtools has parent organization: University of Michigan; Ann Arbor; USA |
PMID:24260225 | Free, Available for download, Freely available | OMICS_01968 | SCR_001683 | rSeqDiff: Detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test | 2026-09-05 06:24:37 | 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.
