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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Circlator Resource Report Resource Website 100+ mentions |
Circlator (RRID:SCR_016058) | software application, data processing software, software toolkit, image analysis software, software resource, alignment software | Software that automates assembly circularization and produces accurate linear representations of circular sequences. It is used for assembling of DNA sequence data of complete bacterial and small eukaryotic genomes. | assembly, sequence, genome, DNA, circularization, accurate, bacteria, erukaryote, tool |
is listed by: Debian is listed by: OMICtools |
Wellcome Trust grant 098051 | PMID:26714481 DOI:10.1186/s13059-015-0849-0 |
Free, Available for download | OMICS_09488 | https://github.com/sanger-pathogens/circlator https://sources.debian.org/src/circlator/ |
SCR_016058 | 2026-02-16 09:48:56 | 321 | ||||||
|
Genome Annotation Generator Resource Report Resource Website 10+ mentions |
Genome Annotation Generator (RRID:SCR_016053) | GAG | software application, data processing software, sequence analysis software, data analysis software, source code, software resource | Command line program to read, modify, annotate and generate genomic data. Can write files to .gff3 or to the NCBI's .tbl format. | genome, annotation, tbl, ncbi, command, line, code, modify, read, annotate, gff3, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download | biotools:gag | https://bio.tools/gag | SCR_016053 | gag.py | 2026-02-16 09:48:56 | 17 | ||||||
|
Phenocarta Resource Report Resource Website 1+ mentions |
Phenocarta (RRID:SCR_016273) | software application, data processing software, data analysis software, software resource, database, data or information resource | Database that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. Part of Gemma, a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data. | phenotype, meta, analysis, genome, gene, expression |
is related to: Gemma has parent organization: University of British Columbia; British Columbia; Canada |
PMID:22782548 | Free, Freely available | http://pavlab.msl.ubc.ca/software-and-resources/ | SCR_016273 | Phenocarta | 2026-02-16 09:49:00 | 2 | |||||||
|
Diabetes Epigenome Atlas Resource Report Resource Website 1+ mentions |
Diabetes Epigenome Atlas (RRID:SCR_016441) | atlas, database, topical portal, portal, data or information resource, disease-related portal | Collects and provides data on the human genome and epigenome to facilitate genetic studies of type 2 diabetes and its complications. A component of the AMP T2D consortium, which includes the National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK) and an international collaboration of researchers. | collect, provide, data, human, genome, epigenome, genetic, study, type 2 diabetes |
has parent organization: Stanford University; Stanford; California has parent organization: University of California at San Diego; California; USA |
type 2 diabetes | NIDDK U01 DK100554 | Free, Proprietary data are available only to approved AMP consortium users with user accounts | SCR_016537 | SCR_016441 | 2026-02-16 09:49:01 | 2 | |||||||
|
IndelGenotyper Resource Report Resource Website 50+ mentions |
IndelGenotyper (RRID:SCR_016663) | GATK | software application, data processing software, sequence analysis software, data analysis software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer. | next, generation, analysis, genomic, data, cancer, genome |
is listed by: Debian has parent organization: Broad Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/broadinstitute/gatk/ https://sources.debian.org/src/gatk/ |
SCR_016663 | GATK Indel Genotyper, Genome Analysis Toolkit (GATK) Indel Genotyper, Indel Genotyper, GATK IndelGenotyper | 2026-02-16 09:49:05 | 63 | |||||||
|
Sequenza Resource Report Resource Website 50+ mentions |
Sequenza (RRID:SCR_016662) | software application, data processing software, data visualization software, data analysis software, software resource | Software package for copy number estimation from tumor genome sequencing data.Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization. | estimate, copy, number, tumor, genome, sequencing, data, cellularity, ploidy, alteration, cancer, mutation, detection, quantification, visualization |
is listed by: CRAN has parent organization: Technical University of Denmark; Lyngby; Denmark |
European Commission 7th Framework Programme ; Danish Council for Independent Research ; Breast Cancer Research Foundation |
PMID:25319062 | https://cran.r-project.org/web/packages/sequenza/ | SCR_016662 | 2026-02-16 09:49:05 | 54 | ||||||||
|
Assemblosis Resource Report Resource Website 1+ mentions |
Assemblosis (RRID:SCR_016571) | software application, data processing software, narrative resource, workflow, training material, software resource, data or information resource | Software tool as a Common Workflow Language (CWL) based automated bioinformatics workflow to assemble haploid/diploid eukaryote genomes of non-model organisms using PacBio long-reads and Illumina short-reads. | common, workflow, language, automated, assemble, haploid, diploid, eukaryote, genome, longread, shortread, data | Free, Available for download, Freely available | SCR_016571 | 2026-02-16 09:49:03 | 1 | |||||||||||
|
Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | software application, data processing software, data analysis software, image analysis software, software resource, alignment software | Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. | sequence, alignment, counting, multi, seed, strategy, mapping, read, reference, genome, analysis, data, SNP, calling, mutation, discovery, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: Subread |
Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | 2026-02-16 09:49:07 | 188 | ||||||
|
MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | data analysis service, analysis service resource, database, production service resource, service resource, data or information 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 | 2026-02-16 09:49:06 | 22 | ||||
|
Supernova assembler Resource Report Resource Website 10+ mentions |
Supernova assembler (RRID:SCR_016756) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software to generate phased, whole genome de novo assemblies from a Chromium prepared library. Used to create true diploid de novo assemblies and can separate homologous chromosomes over long distances. | generate, phased, whole, genome, de novo, assembly, Chromium, prepared, library | is listed by: OMICtools | Free, Available for download, Freely available | https://support.10xgenomics.com/de-novo-assembly/software/pipelines/latest/installation | SCR_016756 | 2026-02-16 09:49:06 | 33 | |||||||||
|
Discovar assembler Resource Report Resource Website 10+ mentions |
Discovar assembler (RRID:SCR_016755) | Discovar | software application, data processing software, sequence analysis software, data analysis software, software resource | 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 | 2026-02-16 09:49:06 | 20 | ||||||
|
Rampart Resource Report Resource Website 1+ mentions |
Rampart (RRID:SCR_016742) | data processing software, software application, software resource, workflow software | Software for workflow management system for de novo genome assembly of DNA sequence data.Designed to exploit high performance computing environments, such as clusters and shared memory systems. | workflow, management, system, de novo, genome, assembly, DNA, sequence, data, high, performance, computing, environment, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: The Genome Analysis Centre; Norwich; United Kingdom |
BBSRC | PMID:25637556 | Free, Available for download, Freely available | biotools:rampart | http://www.earlham.ac.uk/rampart/ https://bio.tools/rampart |
SCR_016742 | 2026-02-16 09:49:06 | 2 | ||||||
|
GenomeScope Resource Report Resource Website 500+ mentions |
GenomeScope (RRID:SCR_017014) | Genomescope | software application, data processing software, data analysis software, software resource, service resource | 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 | 2026-02-16 09:49:08 | 651 | ||||||
|
CPTAC Resource Report Resource Website 100+ mentions |
CPTAC (RRID:SCR_017135) | organization portal, topical portal, consortium, portal, data or information resource, disease-related portal | Clinical proteomic tumor analysis consortium to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, in order to understand molecular basis of cancer that is not possible through genomics and to accelerate translation of molecular findings into clinic. Operates through Proteome Characterization Centers, Proteogenomic Translational Research Centers, and Proteogenomic Data Analysis Centers. CPTAC investigators collaborate, share data and expertise across consortium, and participate in consortium activities like developing standardized workflows for reproducible studies. | identify, protein, alteration, cancer, genome, clinical, study, proteome, proteogenomic, tumor, data, analysis, consortium, reproducibility | has parent organization: National Cancer Institute | cancer | SCR_017135 | Clinical Proteomic Tumor Analysis Consortium | 2026-02-16 09:49:10 | 131 | |||||||||
|
OmicsSIMLA Resource Report Resource Website 1+ mentions |
OmicsSIMLA (RRID:SCR_017011) | software application, software resource, simulation software, software toolkit | Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version. | multi, omics, data, simulator, disease, genomic, epigenomic, transcriptomic, proteomic, genome, sequencing, protein, RNA | is listed by: OMICtools | Ministry of Science and Technology in Taiwan | DOI:10.1101/426510 | Freely available, Available to download, Free | OMICS_31363 | SCR_017011 | 2026-02-16 09:49:08 | 1 | |||||||
|
University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility Resource Report Resource Website |
University of Cambridge Centre for Trophoblast Research Bioinformatics Core Facility (RRID:SCR_017192) | CTR Bioinformatics Core Facility | training service resource, core facility, access service resource, data analysis service, analysis service resource, production service resource, service resource | Core provides assistance with experimental design, RNA sequencing, whole genome and targeted sequencing, methylation sequencing, protein alignment, microscopy image analysis, and training. | bioinformatics, sequencing, RNA, genome, methylation, protein, alignment, data, image, analysis | has parent organization: University of Cambridge; Cambridge; United Kingdom | Restricted | SCR_017192 | Center for Trophoblast Research, Centre for Trophoblast Research, Bioinformatics Core Facility, University of Cambridge | 2026-02-16 09:49:11 | 0 | ||||||||
|
shovill Resource Report Resource Website 100+ mentions |
shovill (RRID:SCR_017077) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit. | assembly, bacteria, isolate, genome, Illumina, paired, end, read, data, haploid, organism, bio.tools |
uses: SPAdes is listed by: Debian is listed by: bio.tools is related to: Trimmomatic is related to: SAMTOOLS is related to: BWA is related to: FLASH is related to: Velvet is related to: Pilon |
Free, Available for download, Freely available | , biotools:shovill, BioTools:shovill | https://bio.tools/shovill https://sources.debian.org/src/shovill/ |
SCR_017077 | 2026-02-16 09:49:09 | 445 | ||||||||
|
rnaSPAdes Resource Report Resource Website 50+ mentions |
rnaSPAdes (RRID:SCR_016992) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software tool for assembling transcripts from RNA-Seq data. Explores surprising computational parallels between assembly of transcriptomes and single cell genomes. Suitable for all kind of organisms. Part of SPAdes package since version 3.9. | assembling, transcript, RNA-Seq, data, single, cell, genome, analysis, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: SPAdes is related to: rnaQUAST |
Russian Science Foundation 14-50-00069 | DOI:10.1101/420208 | Free, Available for download, Freely available | biotools:rnaSPAdes_autogenerated | https://bio.tools/rnaSPAdes_autogenerated | SCR_016992 | 2026-02-16 09:49:08 | 53 | ||||||
|
PathwayNet Resource Report Resource Website 1+ mentions |
PathwayNet (RRID:SCR_017353) | web service, data analysis service, analysis service resource, data access protocol, software resource, production service resource, service 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 | 2026-02-16 09:49:13 | 7 | ||||||||
|
peddy Resource Report Resource Website 10+ mentions |
peddy (RRID:SCR_017287) | software application, data processing software, data analytics software, data analysis software, 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 | 2026-02-16 09:49:12 | 10 |
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