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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.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Bovine Genome Project
 
Resource Report
Resource Website
Bovine Genome Project (RRID:SCR_008370) Bovine Genome Project data analysis service, analysis service resource, data set, data or information resource, production service resource, service resource Downloadable files of the bos taurus genome. Draft assemblies available for download as contigs or linearized scaffolds of the genomic sequence of cow, Bos taurus, including the final draft assembly (7.1 coverage) and the two previous assemblies. The genome is sequenced to 6- to 8-fold sequence depth, with high-quality finished sequence in some areas. Accompanying EST and SNP analyses is also included. The bovine genome assembly and analysis and the study of cattle genetic history were published in April 24, 2009 issue of Science. The Human Genome Sequencing Center provides BLAST searches of the genome assemblies, either as contigs or as linearized chromosome sequences. The WGS sequence enriched BAC assemblies and the unassembled reads (sequencing reads that did not end up in the genome assembly) can also be searched by BLAST. Traces are available from the NCBI Trace Archive by using the link in the sidebar or by using NCBI MegaBLAST with a same species or cross species query. bovine, cattle, cow, genome, genotype, reagent, sequencing, blast, genome assembly, contig, linearized chromosome, single nucleotide polymorphism, bac map, expressed sequence tag has parent organization: Baylor University; Texas; USA NHGRI ;
USDA Agricultural Research Service ;
USDA Cooperative State Research Education and Extension Service ;
State of Texas ;
Genome Canada ;
Genome British Columbia ;
CSIRO ;
Agritech Investments Ltd. New Zealand ;
Dairy Insight Inc. New Zealand ;
AgResearch Ltd.New Zealand ;
Robert J. Kleberg ;
Jr. and Helen C. Kleberg Foundation ;
National Texas and South Dakota Beef Check-off Funds
PMID:19393050 nif-0000-25603 http://www.hgsc.bcm.tmc.edu/project-species-m-Bovine.hgsc?pageLocation=Bovine SCR_008370 2026-02-14 02:01:37 0
ENCODE
 
Resource Report
Resource Website
1000+ mentions
ENCODE (RRID:SCR_006793) data repository, storage service resource, data analysis service, analysis service resource, data or information resource, production service resource, service resource, database Encyclopedia of DNA elements consisting of list of functional elements in human genome, including elements that act at protein and RNA levels, and regulatory elements that control cells and circumstances in which gene is active. Enables scientific and medical communities to interpret role of human genome in biology and disease. Provides identification of common cell types to facilitate integrative analysis and new experimental technologies based on high-throughput sequencing. Genome Browser containing ENCODE and Epigenomics Roadmap data. Data are available for entire human genome. Encyclopedia, DNA, element, functional, human, genome, protein, RNA, level, regulatory, gene, active, disease, analysis uses: Segway - a way to segment the genome
is used by: BioSample Database at EBI
is used by: VizHub
is used by: GEMINI
is used by: Deep Blue Epigenomic Data Server
is recommended by: National Library of Medicine
is listed by: OMICtools
is affiliated with: GENCODE
is related to: Factorbook
is related to: UCSC Genome Browser
is related to: modENCODE
is related to: UCSC Genome Browser
is related to: Encode
has parent organization: University of California at Santa Cruz; California; USA
NHGRI PMID:21526222 Free, Freely available nif-0000-02797, r3d100013051, SCR_017493, OMICS_00532 http://encodeproject.org/ENCODE/
https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements
https://www.encodeproject.org/
https://doi.org/10.17616/R31NJMKB
SCR_006793 ENCODE - Encyclopedia of DNA Elements, ENCODE + Epigenomics Roadmap Combined Data Browser, Encyclopedia of DNA Elements, Encyclopedia of DNA Elements (ENCODE) 2026-02-14 02:01:22 3681
1000 Genomes: A Deep Catalog of Human Genetic Variation
 
Resource Report
Resource Website
5000+ mentions
1000 Genomes: A Deep Catalog of Human Genetic Variation (RRID:SCR_006828) 1000 Genomes portal, consortium, data set, data or information resource, organization portal, database International collaboration producing an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts, in an effort to provide a foundation for investigating the relationship between genotype and phenotype. The genomes of about 2500 unidentified people from about 25 populations around the world were sequenced using next-generation sequencing technologies. Redundant sequencing on various platforms and by different groups of scientists of the same samples can be compared. The results of the study are freely and publicly accessible to researchers worldwide. The consortium identified the following populations whose DNA will be sequenced: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States. The goal Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. Sequencing is still too expensive to deeply sequence the many samples being studied for this project. However, any particular region of the genome generally contains a limited number of haplotypes. Data can be combined across many samples to allow efficient detection of most of the variants in a region. The Project currently plans to sequence each sample to about 4X coverage; at this depth sequencing cannot provide the complete genotype of each sample, but should allow the detection of most variants with frequencies as low as 1%. Combining the data from 2500 samples should allow highly accurate estimation (imputation) of the variants and genotypes for each sample that were not seen directly by the light sequencing. All samples from the 1000 genomes are available as lymphoblastoid cell lines (LCLs) and LCL derived DNA from the Coriell Cell Repository as part of the NHGRI Catalog. The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via their mirrored ftp sites. ftp://ftp.1000genomes.ebi.ac.uk ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes genetic variation, gene, next-generation sequencing, sequence, alignment, genome, single-nucleotide polymorphism, structural variant, haplotype, genome-wide association study, pharmacology, genetics, biomarker, consortium, data sharing, genotype, phenotype, FASEB list uses: NHGRI Sample Repository for Human Genetic Research
is used by: BioSample Database at EBI
is listed by: OMICtools
is listed by: re3data.org
is listed by: Consortia-pedia
is related to: MOSAIK
is related to: ART
is related to: SNAP - SNP Annotation and Proxy Search
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
has parent organization: Harvard Medical School; Massachusetts; USA
has parent organization: Broad Institute
has parent organization: NCBI
has parent organization: European Bioinformatics Institute
has parent organization: National Human Genome Research Institute
Wellcome Trust Sanger Institute; Hinxton; United Kingdom ;
Beijing Genomics Institute; Shenzhen; China ;
NHGRI ;
454 Life Sciences Roche ;
Life Technologies ;
Illumina
Free, Public, Restrictions apply, Http://www.1000genomes.org/data#DataAccess r3d100010180, nlx_143819, OMICS_00261 https://doi.org/10.17616/R3CP4M SCR_006828 International 1000 Genomes Project, 1000 Genomes Project 2026-02-14 02:01:16 5486
eXpress
 
Resource Report
Resource Website
100+ mentions
eXpress (RRID:SCR_006873) eXpress sequence analysis software, data processing software, data analysis software, software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented January 29, 2018.
From website: "Note that the eXpress software is also no longer being developed. We recommend you use kallisto instead." Kallisto can be found at http://pachterlab.github.io/kallisto/.

Software for streaming quantification for high-throughput DNA/RNA sequencing.
Can be used in any application where abundances of target sequences need to be estimated from short reads sequenced from them.
quantification, high-throughput, DNA, RNA, sequencing, target, fragment, analysis is listed by: OMICtools
is listed by: Debian
has parent organization: University of California at Berkeley; Berkeley; USA
NSF ;
NHGRI R01HG006129
DOI:10.1038/nmeth.2251 THIS RESOURCE IS NO LONGER IN SERVICE SCR_015990, OMICS_01275 https://sources.debian.org/src/berkeley-express/ SCR_006873 eXpress - Streaming quantification for high-throughput sequencing, Berkeley-express 2026-02-14 02:01:17 494
DGIdb
 
Resource Report
Resource Website
100+ mentions
DGIdb (RRID:SCR_006608) DGIdb data or information resource, data access protocol, software resource, database, application programming interface A database of drug-gene relationships that provides drug-gene interactions and potential druggability data given list of genes. There are about 15 data sources that are being aggregated by DGIdb, with update date and these data sources are listed on this page: http://dgidb.genome.wustl.edu/sources, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. drug, gene, interaction, bio.tools, FASEB list is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Washington University in St. Louis; Missouri; USA
Cancer NHGRI U54 HG003079 PMID:24122041 THIS RESOURCE IS NO LONGER IN SERVICE nlx_155686, biotools:DGIdb, OMICS_01579 https://bio.tools/DGIdb SCR_006608 Drug-Gene Interaction database, Drug Gene Interaction Database 2026-02-14 02:01:12 353
Consensus Measures for Phenotype and Exposure
 
Resource Report
Resource Website
1+ mentions
Consensus Measures for Phenotype and Exposure (RRID:SCR_006688) PhenX knowledge environment THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 05 01 2025. PhenX is a project to prioritize Phenotype and eXposure measures for Genome-wide Association Studies (GWAS). Leaders of the scientific community will assess and prioritize a broad range of domains relevant to genomics research and public health. The PhenX Steering Committee (SC), chaired by Dr. Jonathan Haines, provides leadership in the selection of domains and domain experts. Members of the SC include outstanding scientists from the research community and liaisons from the Institutes and Centers of the National Institutes of Health. Consensus measures for GWAS will have a direct impact on biomedical research and ultimately on public health. During the course of this project, up to 20 research domains will be examined, with up to 15 measures being recommended for use in future GWAS and other large-scale genomic research efforts. The goal is to maximize the benefits of future research by having comparable measures so that studies can be integrated. Each selected domain will be reviewed by a Working Group (WG) of scientists who are experts in the research area. A systematic review of the literature will guide the WGs selection of up to 15 high priority measures with standardized approaches for measurement. Selection criteria for the measures include factors such as validity, reproducibility, cost, feasibility, and burden to both investigators and participants. The scientific community will be asked to provide input on proposed measures. Consensus development is a key component of the project. biomedical, domain, genome, health, phenotype, public, research has parent organization: RTI International
is parent organization of: Phenotypes and eXposures Toolkit
is parent organization of: PhenX Phenotypic Terms
has organization facet: Phenotypes and eXposures Toolkit
NHGRI U01 HG004597 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-32816 SCR_006688 PhenX - consensus measures for Phenotypes and eXposures, Consensus Measures for Phenotypes Exposures, PhenX (consensus measures for Phenotypes and eXposures), Consensus Measures for Phenotypes Exposure, Consensus Measures for Phenotypes and Exposures 2026-02-14 02:01:22 1
FLASH
 
Resource Report
Resource Website
1000+ mentions
FLASH (RRID:SCR_005531) FLASh sequence analysis software, data processing software, data analysis software, software application, software resource Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data. bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: shovill
is related to: CLIP-Explorer
has parent organization: Johns Hopkins University; Maryland; USA
NLM R01 LM006845;
NIGMS R01 GM083873;
NHGRI R01 HG006677
PMID:21903629 Free, Available for download, Freely available biotools:flash, OMICS_01047 https://sourceforge.net/projects/flashpage/files/
https://bio.tools/flash
https://sources.debian.org/src/flash/
SCR_005531 Fast Length Adjustment of SHort reads, Fast Length Adjustment of Short reads 2026-02-14 02:00:55 2175
Consed
 
Resource Report
Resource Website
500+ mentions
Consed (RRID:SCR_005650) Consed software resource A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence) next-generation sequencing, graphical editor, linux, macosx, solaris, c++ is listed by: OMICtools
has parent organization: University of Washington; Seattle; USA
NIH ;
NHGRI R01HG005710
PMID:23995391
PMID:9521923
Free for academic use, Free for non-profit use, Commercial license OMICS_00879 SCR_005650 2026-02-14 02:01:08 595
PubSearch
 
Resource Report
Resource Website
1+ mentions
PubSearch (RRID:SCR_005830) PubSearch data or information resource, software resource, service resource, database THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. PubSearch is a web-based literature curation tool, allowing curators to search and annotate genes to keywords from articles. It has a simple mySQL database backend and uses a set of Java Servlets and JSPs for querying, modifying, and adding gene, gene-annotation, and literature information. PubSearch can be downloaded from GMOD. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible gene, annotate, editor, literature curation tool, literature, ontology or annotation editor is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: TAIR
has parent organization: Stanford University; Stanford; California
NHGRI R01HG02728 THIS RESOURCE IS NO LONGER IN SERVICE nlx_149338 SCR_005830 2026-02-14 02:00:59 1
GeneTests
 
Resource Report
Resource Website
10+ mentions
GeneTests (RRID:SCR_010725) GeneTests portal, analysis service resource, material analysis service, data or information resource, production service resource, biomaterial analysis service, service resource, narrative resource, training material, topical portal, database 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 2026-02-14 02:02:04 12
MAPP
 
Resource Report
Resource Website
50+ mentions
MAPP (RRID:SCR_010775) MAPP software resource Java program that predicts the impact of all possible amino acid substitutions on the function of the protein., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. is listed by: OMICtools
has parent organization: Stanford University; Stanford; California
NHGRI THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00132 SCR_010775 Multivariate Analysis of Protein Polymorphism, Multivariate Analysis of Protein Polymorphism:MAPP 2026-02-14 02:02:05 58
ASprofile
 
Resource Report
Resource Website
10+ mentions
ASprofile (RRID:SCR_001833) ASprofile software resource A suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data. alternative splicing event, rna-seq, alternative splicing is listed by: OMICtools
has parent organization: Johns Hopkins University; Maryland; USA
NHGRI R01-HG006677 PMID:24555089 Free, Available for download, Freely available OMICS_01942 SCR_001833 2026-02-14 02:00:08 37
MouseCyc
 
Resource Report
Resource Website
1+ mentions
MouseCyc (RRID:SCR_001791) MouseCyc data analysis service, analysis service resource, data or information resource, production service resource, service resource, database A manually curated database of both known and predicted metabolic pathways for the laboratory mouse. It has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways with 1,790 compounds and 1,122 enzymatic reactions in MouseCyc. (Aug. 2013) BLAST and other tools are available. The initial focus for the development of MouseCyc is on metabolism and includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of biological knowledge for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database. energy production, biosynthesis, cell, cellular, degradation, detoxification, metabolism, mouse, physiological, enzymatic reaction, gene, disease, genome, metabolic pathway, pathway, compound, enzymatic reaction, protein, rna, reaction, blast, human, mammal, genetic, genomic is related to: Mouse Genome Informatics (MGI)
is related to: Gene Ontology
has parent organization: Jackson Laboratory
NHGRI HG003622 PMID:19682380 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-10303 SCR_001791 MouseCyc database, Mouse Genome Informatics: MouseCyc database 2026-02-14 02:00:11 9
SPP
 
Resource Report
Resource Website
1+ mentions
SPP (RRID:SCR_001790) data analysis software, software resource, data processing software, software application R analysis and processing package for Illumina platform Chip-Seq data. chip seq data, illummina, r package, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
NHGRI U01HG004258;
NIGMS R01GM082798;
NCRR UL1RR024920
DOI:10.1038/nbt.1508 Free, Available for download, Freely available OMICS_00425, biotools:spp https://bio.tools/spp https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq SCR_001790 SPP Package 2026-02-14 02:00:08 9
Bowtie 2
 
Resource Report
Resource Website
1000+ mentions
Bowtie 2 (RRID:SCR_016368) sequence analysis software, data processing software, alignment software, data analysis software, software application, software resource, image analysis software Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method. sequence, analysis, long, reference, sequence, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools is used by: HLA-HD
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: Bowtie
NHGRI R01 HG006102;
NIGMS R01 GM083873
PMID:22388286 Free, Available for download, Freely available biotools:bowtie2 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
https://github.com/BenLangmead/bowtie2
https://bio.tools/bowtie2
SCR_016368 , bowtie 2, bowtie2 v 2.2.3 2026-02-14 02:02:42 1745
PathwayNet
 
Resource Report
Resource Website
1+ mentions
PathwayNet (RRID:SCR_017353) web service, data analysis service, analysis service resource, production service resource, service resource, data access protocol, software resource Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks. Interface, interaction, predict, human, gene, network, integrative, analysis, user, data, tissue, cell, functional, protein, genome is listed by: OMICtools
has parent organization: Princeton University; New Jersey; USA
NIGMS R01 GM071966;
NHGRI HG005998;
NIGMS P50 GM071508
PMID:25431329 Free, Freely available SCR_017353 2026-02-14 02:03:11 7
peddy
 
Resource Report
Resource Website
10+ mentions
peddy (RRID:SCR_017287) data processing software, data analysis software, data analytics software, software application, software resource Software package that evaluates correspondence between stated sexes, relationships, and ancestries in pedigree file and those inferred from genotypes in VCF file resulting from human whole genome sequencing or whole exome sequencing studies. Facilitates both automated and interactive, visual detection of sample swaps, poor sequencing quality, and other indicators of sample problems. sex, relation, ancestry, evaluate, pedigree, VCF file, genome, sequencing, exome, error, genotype has parent organization: University of Utah; Utah; USA NHGRI R01 HG006693 PMID:28190455 Free, Available for download, Freely available http://quinlanlab.org/#portfolioModal8 SCR_017287 2026-02-14 02:03:18 10
GeneMarkS-T
 
Resource Report
Resource Website
100+ mentions
GeneMarkS-T (RRID:SCR_017648) data analysis software, software resource, data processing software, software application Software package for ab initio identification of protein coding regions in RNA transcripts. Algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. Sets of assembled eukaryotic transcripts can be analyzed by modified GeneMarkS-T algorithm which part of gene prediction programs GeneMark. Identification, protein, coding, region, RNA, transcript, gene, discovery, eukaryotic, sequence, bio.tools is listed by: Debian
is listed by: bio.tools
has parent organization: Georgia Institute of Technology; Georgia; USA
NHGRI HG000783 PMID:25870408 Restricted biotools:GeneMarkS-t https://bio.tools/GeneMarkS-T SCR_017648 2026-02-14 02:03:30 113
Computing Genome Assembly Likelihoods
 
Resource Report
Resource Website
100+ mentions
Computing Genome Assembly Likelihoods (RRID:SCR_017624) CGAL data processing software, alignment software, software application, software resource, image analysis software Software tool for computing genome assembly likelihoods.Computes likelihood of reads with respect to assembly and statistical model which can be used as metric for evaluating assemblies. Novel likelihood based approach to assembly assessment in absence of ground truth. Computing, genome, assembly, likelihood, read, evaluation NHGRI R21 HG006583;
Fulbright Science & Technology Fellowship
PMID:23360652 http://bio.math.berkeley.edu/cgal/ SCR_017624 2026-02-14 02:03:14 106
FastProject
 
Resource Report
Resource Website
FastProject (RRID:SCR_017462) data visualization software, data processing software, data analysis software, software application, software resource Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored. Two, dimensional, data, reduction, single, cell, RNA seq, visualization, gene, expression, matrix, report, explore, BRAIN Initiative, bio.tools is recommended by: BRAIN Initiative
is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
is related to: University of California at Berkeley; Berkeley; USA
National Institutes of Health NRSA Trainee appointment ;
California Research Alliance by BASF ;
NIMH U01 MH105979;
NHGRI U01 HG007910
PMID:27553427 Free, Available for download, Freely available biotools:fastproject https://bio.tools/fastproject SCR_017462 2026-02-14 02:03:12 0

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