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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BMAP - Brain Molecular Anatomy Project Resource Report Resource Website 1+ mentions |
BMAP - Brain Molecular Anatomy Project (RRID:SCR_008852) | BMAP | funding resource, topical portal, data or information resource, portal | The Brain Molecular Anatomy Project is a trans-NIH project aimed at understanding gene expression and function in the nervous system. BMAP has two major scientific goals: # Gene discovery: to catalog of all the genes expressed in the nervous system, under both normal and abnormal conditions. # Gene expression analysis: to monitor gene expression patterns in the nervous system as a function of cell type, anatomical location, developmental stage, and physiological state, and thus gain insight into gene function. In pursuit of these goals, BMAP has launched several initiatives to provide resources and funding opportunities for the scientific community. These include several Requests for Applications and Requests for Proposals, descriptions of which can be found in this Web site. BMAP is also in the process of establishing physical and electronic resources for the community, including repositories of cDNA clones for nervous system genes, and databases of gene expression information for the nervous system. Most of the BMAP initiatives so far have focused on the mouse as a model species because of the ease of experimental and genetic manipulation of this organism, and because many models of human disease are available in the mouse. However, research in humans, other mammalian species, non-mammalian vertebrates, and invertebrates is also being funded through BMAP. For the convenience of interested investigators, we have established this Web site as a central information resource, focusing on major NIH-sponsored funding opportunities, initiatives, genomic resources available to the research community, courses and scientific meetings related to BMAP initiatives, and selected reports and publications. When appropriate, we will also post initiatives not directly sponsored by BMAP, but which are deemed relevant to its goals. Posting decisions are made by the Trans-NIH BMAP Committee |
has parent organization: National Institutes of Health is parent organization of: BMAP cDNA Resources |
Aging | NINDS ; NIMH ; NIDA ; NEI ; NIA ; NIAAA ; NICHD ; NIDCD ; NIEHS ; NHGRI ; NIGMS |
nlx_149083 | SCR_008852 | Brain Molecular Anatomy Project, Trans-NIH Brain Molecular Anatomy Project | 2026-02-15 09:19:58 | 6 | |||||||
|
GeneTests Resource Report Resource Website 10+ mentions |
GeneTests (RRID:SCR_010725) | GeneTests | portal, database, training material, service resource, production service resource, data or information resource, material analysis service, narrative resource, biomaterial analysis service, topical portal, analysis service resource | The GeneTests Web site, a publicly funded medical genetics information resource developed for physicians, other healthcare providers, and researchers, is available at no cost to all interested persons. By providing current, authoritative information on genetic testing and its use in diagnosis, management, and genetic counseling, GeneTests promotes the appropriate use of genetic services in patient care and personal decision making. At This Site: * GeneReviews: Expert-authored peer-reviewed disease descriptions * Laboratory Directory: International directory of genetic testing laboratories * Clinic Directory: International directory of genetics and prenatal diagnosis clinics * Educational Materials: Illustrated glossary, information on genetic services, PowerPoint presentations, annotated Internet resources We comply with the HONcode standard for trustworthy health information. |
has parent organization: University of Washington; Seattle; USA has parent organization: NCBI |
NCI ; NHGRI 1 P41 LM/HG 06029; NLM 1 P41 LM/HG 06029; NLM contract N01-LM-4-3505; NLM 5 P41 LM07242; NLM 2 P41 LM 06001; DOE DE-FG03-02ER63301/A00 |
nlx_94696 | SCR_010725 | GeneTests: Clinical Genetic Information Resource | 2026-02-15 09:20:21 | 12 | ||||||||
|
MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | software application, data processing software, data analysis software, software resource | Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity. | identify, transcript, factor, binding, site, model, based, analysis, CHIP Seq, short, read, sequencer, protein, DNA, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Dana-Farber Cancer Institute |
NHGRI HG004069; NHGRI HG004270; NIDDK DK074967 |
PMID:18798982 DOI:10.1186/gb-2008-9-9-r137 |
Free, Available for download, Freely available | OMICS_00446, biotools:macs | https://bio.tools/macs https://sources.debian.org/src/macs/ |
SCR_013291 | MACS - Model-based Analysis for ChIP-Seq, Model-based Analysis for ChIP-Seq, MACS2 | 2026-02-15 09:20:42 | 1325 | ||||
|
AbundantOTU+ Resource Report Resource Website 1+ mentions |
AbundantOTU+ (RRID:SCR_016527) | AbundantOTU | software application, sequence analysis software, data processing software, software resource, data analysis software | Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset. | pyrosequencing, 16S, rRNA, gene, operational, taxonomic, unit, abundant, species, dataset |
is listed by: OMICtools has parent organization: Indiana University; Indiana; USA |
NHGRI R01 HG004908; NHLBI U01 HL09896001 |
PMID:22102981 | Free, Available for download, Freely available | SCR_016527 | AbundantOTU:Abundant Operational Taxonomic Unit, Abundant OTU, AbundantOTU+ | 2026-02-15 09:21:52 | 1 | ||||||
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biobakery Resource Report Resource Website 10+ mentions |
biobakery (RRID:SCR_016596) | software application, data processing software, software resource, software toolkit, data analysis software | Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Huttenhower lab, metaomics, data, analysis, process, raw, shotgun, metagenome, metatranscriptome, sequencing, microbial, profiling, bio.tools |
is used by: Nephele is listed by: Debian is listed by: bio.tools is related to: Human Microbiome Project has parent organization: Harvard University; Cambridge; United States |
NIDDK U54 DE023798; Sloan Foundation 4406J0B; NHGRI R01 HG005220; NSF DBI1053486; NHGRI R01 HG005969; ARO W911NF1110473 |
PMID:29194469 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:biobakery | http://huttenhower.sph.harvard.edu/biobakery https://bio.tools/biobakery |
SCR_016596 | bioBakery, biobakery | 2026-02-15 09:21:53 | 13 | |||||
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LINCS Project Resource Report Resource Website 10+ mentions |
LINCS Project (RRID:SCR_016486) | LINCS | organization portal, portal, database, consortium, project portal, data or information resource | Project to create network based understanding of biology by cataloging changes in gene expression and other cellular processes when cells are exposed to genetic and environmental stressors. Program to develop therapies that might restore pathways and networks to their normal states. Has LINCS Data Coordination and Integration Center and six Data and Signature Generation Centers: Drug Toxicity Signature Generation Center, HMS LINCS Center, LINCS Center for Transcriptomics, LINCS Proteomic Characterization Center for Signaling and Epigenetics, MEP LINCS Center, and NeuroLINCS Center. | data integration, network biology, gene expression, L1000, MCF10A, MEMA, P100, LINCS program, LINCS project, systems biology, systems pharmacology, FASEB list |
is related to: Drug Gene Budger is related to: LINCS Joint Project - Breast Cancer Network Browser is related to: piNET |
cancer, heart disease, neurodegenerative disorder | NIH Common Fund ; NHLBI U54 HL127624; NHLBI U54 HL127366; NHLBI U54 HL127365; NHGRI U54 HG008100; NHGRI U54 HG008097; NHGRI U54 HG008098; NINDS U54 NS091046 |
PMID:29199020 | Free, Freely available | SCR_016487 | SCR_016486 | LINCS, Library of Integrated Network based Cellular Signatures, LINCS Program | 2026-02-15 09:21:52 | 43 | ||||
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MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | data analysis service, database, service resource, production service resource, data or information resource, analysis service resource | Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research. | integration, database, model, genetic, resource, functional, annotation, genome, data, analysis, dataset, rare, variant, exploration, bio.tools |
uses: OMIM uses: ClinVar uses: DECIPHER uses: Geno2MP uses: Database of Genomic Variants is used by: Hypothesis Center is listed by: bio.tools is listed by: Debian |
NINDS 1U54NS093793; NIH Office of the Director R24 OD022005; The Robert and Janice McNair Foundation ; Baylor College of Medicine Medical Scientist Training Program ; NINDS U54 NS093793; NIGMS R01 GM067858; NIGMS R01 GM120033; NSF DMS 1263932; CPRIT RP170387; Houston Endowment ; Huffington Foundation ; Belfer Foundation ; T T Chao Family Foundation ; NIGMS R01 GM067761; NIGMS R01 GM084947; NCRR R24 RR032668; NIH Office of the Director R24 OD021997; NCI P30 CA06516; NHGRI U01 HG007709; Simons Foundation |
PMID:28502612 | Free, Public, Freely available | biotools:marrvel | https://bio.tools/marrvel | SCR_016871 | Model organism Aggregated Resources for Rare Variant ExpLoration | 2026-02-15 09:21:49 | 22 | ||||
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Discovar assembler Resource Report Resource Website 10+ mentions |
Discovar assembler (RRID:SCR_016755) | Discovar | software application, sequence analysis software, data processing software, software resource, data analysis software | Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes. | variant, calling, reference, de novo, assembly, genome, genetic, human, sequence, analysis |
is listed by: OMICtools has parent organization: Broad Institute |
NHGRI R01 HG003474; NHGRI U54 HG003067; NIAID HHSN272200900018C |
PMID:25326702 | Free, Available for download, Freely available | SCR_016755 | Discovar de novo, Discovar | 2026-02-15 09:21:49 | 20 | ||||||
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PathwayMatcher Resource Report Resource Website 1+ mentions |
PathwayMatcher (RRID:SCR_016759) | software application, data processing software, software resource, network analysis software, data analysis software | Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome. | mapping, omics, data, pathways, network, analysis, proteoform, generate, Reactome, database, match, bio.tools |
is listed by: Galaxy is listed by: OMICtools is listed by: Debian is listed by: bio.tools works with: Reactome |
European Research Council ; Research Council of Norway ; Bergen Research Foundation ; NIGMS U54 GM114833; NHGRI U41 HG003751 |
DOI:10.1101/375097 | Free, Available for download, Freely available | BioTools:PathwayMatcher, biotools:PathwayMatcher | https://anaconda.org/bioconda/pathwaymatcher https://toolshed.g2.bx.psu.edu/repository?repository_id=6d75f02b86acc421 https://bio.tools/PathwayMatcher https://bio.tools/PathwayMatcher https://bio.tools/PathwayMatcher |
SCR_016759 | 2026-02-15 09:21:10 | 1 | ||||||
|
Sashimiplot Resource Report Resource Website |
Sashimiplot (RRID:SCR_016861) | sashimiplot | software application, data visualization software, data processing software, software resource | Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. | quantitative, visualization, aligned, RNA-Seq, read, data, compare, exon, usage, sample, experiment, condition, MISO | is related to: MISO | NCI R01 CA157304; Starr Cancer Consortium ; NIGMS R01 GM096193; NSF IIS 1149662; Alfred P. Sloan research fellowship ; NIGMS R01 GM085319; NCI U01 CA184897; NHGRI R01 HG002439 |
PMID:25617416 DOI:10.1093/bioinformatics/btv034 |
Free, Available for download, Freely available | http://miso.readthedocs.org/en/fastmiso/sashimi.html | SCR_016861 | sashimi_plot | 2026-02-15 09:21:11 | 0 | |||||
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GenomicFeatures Resource Report Resource Website 50+ mentions |
GenomicFeatures (RRID:SCR_016960) | software application, data processing software, software resource, software toolkit, data analysis software | Software R package for making and manipulating transcript centric annotations. Used to download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database. | making, manipulating, transcript, centric, annotation, genomic, location, exon, cds, bio.tools |
is used by: riboWaltz is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
NHGRI P41 HG004059; NHGRI U41 HG004059; NHLBI R01 HL086601; NHLBI R01 HL093076; NHLBI R01 HL094635 |
PMID:23950696 | Free, Available for download, Freely available | biotools:genomicfeatures | https://bio.tools/genomicfeatures | SCR_016960 | 2026-02-15 09:21:12 | 65 | ||||||
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GenomeScope Resource Report Resource Website 500+ mentions |
GenomeScope (RRID:SCR_017014) | Genomescope | software application, data processing software, software resource, service resource, data analysis software | Open source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach. | genome, unassembled, sequenced, data, short, read, analysis, heterozygosity, repeat, content, size, kmer | is related to: Cold Spring Harbor Laboratory | NSF DBI 1350041; NSF IOS 1237880; NHGRI R01 HG006677 |
PMID:28369201 | Free, Freely available, | http://qb.cshl.edu/genomescope/ | SCR_017014 | 2026-02-15 09:21:53 | 651 | ||||||
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sleuth Resource Report Resource Website 10+ mentions |
sleuth (RRID:SCR_016883) | software application, data processing software, data analysis software, software resource | Software tool for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. Used for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. | differential, analysis, RNA-Seq, data, gene, expression, bootstrapping, error, linear, modeling, decouple, biological, variance, inferential, bio.tools |
is listed by: Debian is listed by: bio.tools works with: kallisto |
NIDDK R01 DK094699; NHGRI R01 HG006129 |
PMID:28581496 | Free, Available for download, Freely available | biotools:sleuth, BioTools:sleuth | https://bio.tools/sleuth https://bio.tools/sleuth https://bio.tools/sleuth |
SCR_016883 | 2026-02-15 09:21:55 | 24 | ||||||
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Genomic Ranges Resource Report Resource Website 1+ mentions |
Genomic Ranges (RRID:SCR_017051) | software application, data processing software, software resource, software toolkit, data analysis software | Software R package for computing and annotating genomic ranges. Used for storing and manipulating genomic intervals and variables defined along genome. | computing, annotating, genomic, range, storing, manipulating, interval, variable, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
NHGRI P41 HG004059; NHGRI U41 HG004059; NHLBI R01 HL086601; NHLBI R01 HL093076; NHLBI R01 HL094635 |
PMID:23950696 | Free, Available for download, Freely available | biotools:genomicranges | https://bio.tools/genomicranges | SCR_017051 | 2026-02-15 09:21:14 | 2 | ||||||
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Salmon Resource Report Resource Website 100+ mentions |
Salmon (RRID:SCR_017036) | software application, data processing software, data analysis software, software resource | Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias. | quantifying, expression, transcript, RNAseq, data, correct, fragment, GC, content, bias |
is listed by: Debian is listed by: OMICtools has parent organization: Stony Brook University; New York; USA has parent organization: Carnegie Mellon University; Pennsylvania; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: Harvard University; Cambridge; Massachusetts |
Gordon and Betty Moore Foundation Data-Driven Discovery Initiative ; NHGRI R21 HG006913; NHGRI R01 HG007104; Alfred P. Sloan Research ; NCI T32 CA009337; NHGRI R01 HG005220; NSF BIO-1564917; NSF CCF-1256087; NSF CCF-1053918; NSF EF-0849899 |
PMID:28263959 | Free, Available for download, Freely available | OMICS_09075 | https://github.com/COMBINE-lab/salmon https://sources.debian.org/src/salmon/ |
SCR_017036 | 2026-02-15 09:21:14 | 357 | ||||||
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Combined Annotation Dependent Depletion Resource Report Resource Website 500+ mentions |
Combined Annotation Dependent Depletion (RRID:SCR_018393) | CADD | software application, sequence analysis software, data processing software, software resource, data access protocol, web service, service resource, data analysis software | Web tool for predicting deleteriousness of variants throughout human genome. Software tool for scoring deleteriousness of single nucleotide variants as well as insertion and deletions variants in human genome. | Human genome, disease, prediction, injurious variant, single nucleotide variant, insertion variant, deletion variant, deleteriousness scoring | has parent organization: University of Washington; Seattle; USA | NCI R01 CA197139; NHGRI U54 HG006493; Brotman Baty Institute for Precision Medicine ; Berlin Institute of Health ; Howard Hughes Medical Institute ; German Research Foundation ; Charite University Medicine Berlin |
PMID:30371827 PMID:24487276 |
Restricted | SCR_018393 | Combined Annotation Dependent Depletion | 2026-02-15 09:22:13 | 579 | ||||||
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LRPath Resource Report Resource Website 1+ mentions |
LRPath (RRID:SCR_018572) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data. | Gene, map, gene set, gene set testing, identifying enriched biologically group, gene expression data, gene expression, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIEHS P30 ES06096; NIEHS U01 ES015675; NHGRI R01 HG003749; NLM R01 LM008106; NIDA U54 DA021519 |
PMID:19038984 | Free, Freely available | biotools:lrpath | https://bio.tools/lrpath | SCR_018572 | 2026-02-15 09:22:16 | 4 | ||||||
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BRAKER Resource Report Resource Website 100+ mentions |
BRAKER (RRID:SCR_018964) | software application, simulation software, software resource | Software tool as pipeline for accurate and automated gene prediction in novel eukaryotic genomes. Automated gene prediction training and gene prediction pipeline.BRAKER1 is eukaryotic genome annotation pipeline. BRAKER2 is extension of BRAKER1 which allows for fully automated training of gene prediction tools GeneMark EX R14, R15, R17, F1 and AUGUSTUS from RNA Seq and/or protein homology information, and that integrates extrinsic evidence from RNA-Seq and protein homology information into prediction. | Automated gene prediction, novel eukaryotic genomes, gene prediction training, gene prediction pipeline, protein coding gene structure, gene structure prediction, eukaryotic genome, RNA-Seq, protein homology |
uses: Augustus is listed by: Debian is listed by: OMICtools |
NHGRI HG000783; German Research Foundation |
PMID:31020555 DOI:10.1101/2020.08.10.245134 |
Free, Available for download, Freely available | OMICS_10582 | https://sources.debian.org/src/braker/ | SCR_018964 | BRAKER2, BRAKER1 | 2026-02-15 09:22:20 | 458 | |||||
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CHOPCHOP Resource Report Resource Website 1000+ mentions |
CHOPCHOP (RRID:SCR_015723) | software application, web application, software resource, authoring tool | Web application for designing gRNAs for CRISPR/Cas9 experiments. It selects target sites for CRISPR/Cas9, CRISPR/Cpf1 or TALEN-directed mutagenesis. | mutagenesis, talen, grna, crispr, cas9, cpf1, experiment design, target site, genetic engineering | NHGRI P50 HG005550 | PMID:24861617 PMID:27185894 |
Freely available | SCR_015723 | CHOPCHOP v2 | 2026-02-15 09:21:23 | 1652 | ||||||||
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Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | data management software, software application, data processing software, software resource, software toolkit, data analysis software | Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. | c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG004719; NHGRI RC2 HG005552 |
PMID:21493652 DOI:10.1093/bioinformatics/btr174 |
biotools:bamtools, OMICS_11315 | https://bio.tools/bamtools https://sources.debian.org/src/bamtools/ |
SCR_015987 | API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map | 2026-02-15 09:21:30 | 324 |
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