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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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GeneWindow Resource Report Resource Website 1+ mentions |
GeneWindow (RRID:SCR_008183) | data analysis software, software application, data processing software, software resource | Software tool for pre- and post-genetic bioinformatics and analytical work, developed and used at the Core Genotyping Facility (CGF) at the National Cancer Institute. While Genewindow is implemented for the human genome and integrated with the CGF laboratory data, it stands as a useful tool to assist investigators in the selection of variants for study in vitro, or in novel genetic association studies. The Genewindow application and source code is publicly available for use in other genomes, and can be integrated with the analysis, storage, and archiving of data generated in any laboratory setting. This can assist laboratories in the choice and tracking of information related to genetic annotations, including variations and genomic positions. Features of GeneWindow include: -Intuitive representation of genomic variation using advanced web-based graphics (SVG) -Search by HUGO gene symbol, dbSNP ID, internal CGF polymorphism ID, or chromosome coordinates -Gene-centric display (only when a gene of interest is in view) oriented 5 to 3 regardless of the reference strand and adjacent genes -Two views, a Locus Overview, which varies in size depending on the gene or genomic region being viewed and, below it, a Sequence View displaying 2000 base pairs within the overview -Navigate the genome by clicking along the gene in the Locus Overview to change the Sequence View, expand or contract the genomic interval, or shift the view in the 5 or 3 direction (relative to the current gene) -Lists of available genomic features -Search for sequence matches in the Locus Overview -Genomic features are represented by shape, color and opacity with contextual information visible when the user moves over or clicks on a feature -Administrators can insert newly-discovered polymorphisms into the Genewindow database by entering annotations directly through the GUI -Integration with a Laboratory Information Management System (LIMS) or other databases is possible | gene, genetic, analysis, annotation, archive, bioinformatic, cancer, genome, genomic, genotype, genotyping, human, human genome databases, maps, polymorphism, position, variation, data set |
is listed by: 3DVC has parent organization: National Cancer Institute |
nif-0000-21173 | SCR_008183 | GeneWindow | 2026-02-17 10:01:11 | 1 | |||||||||
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Distributed Annotation System Resource Report Resource Website 10+ mentions |
Distributed Annotation System (RRID:SCR_008427) | data or information resource, narrative resource, standard specification, software resource | The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. The advantages of this system are that control over the data is retained by data providers, data is freed from the constraints of specific organisations and the normal issues of release cycles, API updates and data duplication are avoided. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. A DAS-enabled website or application can aggregate complex and high-volume data from external providers in an efficient manner. For the biologist, this means the ability to plug in the latest data, possibly including a user''s own data. For the application developer, this means protection from data format changes and the ability to add new data with minimal development cost. Here are some examples of DAS-enabled applications or websites for end users: :- Dalliance Experimental Web/Javascript based Genome Viewer :- IGV Integrative Genome Viewer java based browser for many genomes :- Ensembl uses DAS to pull in genomic, gene and protein annotations. It also provides data via DAS. :- Gbrowse is a generic genome browser, and is both a consumer and provider of DAS. :- IGB is a desktop application for viewing genomic data. :- SPICE is an application for projecting protein annotations onto 3D structures. :- Dasty2 is a web-based viewer for protein annotations :- Jalview is a multiple alignment editor. :- PeppeR is a graphical viewer for 3D electron microscopy data. :- DASMI is an integration portal for protein interaction data. :- DASher is a Java-based viewer for protein annotations. :- EpiC presents structure-function summaries for antibody design. :- STRAP is a STRucture-based sequence Alignment Program. Hundreds of DAS servers are currently running worldwide, including those provided by the European Bioinformatics Institute, Ensembl, the Sanger Institute, UCSC, WormBase, FlyBase, TIGR, and UniProt. For a listing of all available DAS sources please visit the DasRegistry. Sponsors: The initial ideas for DAS were developed in conversations with LaDeana Hillier of the Washington University Genome Sequencing Center. | annotation, database, software, genomic, protein, sequence, visualization, data, client-server, integration, bioinformatics, genome, structure, data integration |
is listed by: 3DVC has parent organization: Uppsala University; Uppsala; Sweden |
Howard Hughes Medical Institute ; NHGRI 2-P01-HG00956 |
nif-0000-30177 | SCR_008427 | BioDAS | 2026-02-17 10:01:21 | 11 | ||||||||
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Augustus Resource Report Resource Website 1000+ mentions |
Augustus (RRID:SCR_008417) | software application, web application, data processing software, data analysis software, software resource, sequence analysis software | Software for gene prediction in eukaryotic genomic sequences. Serves as a basis for further steps in the analysis of sequenced and assembled eukaryotic genomes. | software, gene, prediction, eucaryotic, genomic, sequence |
is used by: BRAKER is used by: BRO_annotation is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: Gsnap2Augustus |
Deutsche Forschungsgemeinschaft (DFG) HO4545/1-1;; STA1009/6-1 ; Institute for Mathematics and Computer Science ; Ernst Moritz Arndt University of Greifswald |
PMID:23700307 DOI:10.1093/bioinformatics/btw494 |
Free, Available for download, Freely available | SCR_015981, OMICS_07777, nif-0000-30133 | https://sources.debian.org/src/autodock-vina/ | SCR_008417 | Augustus: Gene Prediction, WebAUGUSTUS, Augustus, Augustus [gene prediction] | 2026-02-17 10:01:14 | 3542 | |||||
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Ontology for Genetic Interval Resource Report Resource Website |
Ontology for Genetic Interval (RRID:SCR_003423) | OGI | data or information resource, ontology, controlled vocabulary | An ontology that formalized the genomic element by defining an upper class genetic interval using BFO as its framework. The definition of genetic interval is the spatial continuous physical entity which contains ordered genomic sets (DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure. | owl, genomic, genetic, dna, rna, allele, marker, chromosome, rna molecule |
is listed by: BioPortal is listed by: OBO is listed by: Google Code is related to: Information Artifact Ontology |
Free, Available for download, Freely available | nlx_157517 | https://bioportal.bioontology.org/ontologies/OGI | SCR_003423 | 2026-02-17 10:00:10 | 0 | |||||||
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SOURCE Resource Report Resource Website 50+ mentions |
SOURCE (RRID:SCR_005799) | SOURCE | data or information resource, production service resource, analysis service resource, database, service resource, data analysis service | SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool | genomic, functional annotation, ontology, gene expression, gene, genome, statistical analysis, bio.tools, FASEB list |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: SMD |
NIGMS ; NCI CA85129-04; NIGMS GM07365 |
PMID:12519986 | Restricted | biotools:source, nlx_149287 | https://login.stanford.edu/idp/profile/SAML2/Redirect/SSO?execution=e1s1 https://bio.tools/source |
SCR_005799 | 2026-02-17 10:00:39 | 69 | |||||
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UC Davis Genome Center Labs and Facilities Resource Report Resource Website 1+ mentions |
UC Davis Genome Center Labs and Facilities (RRID:SCR_012480) | UCD Genome Center Labs & Facilities, UCD Genome Center Labs and Facilities | training service resource, organization portal, data or information resource, access service resource, service resource, core facility, portal | Genome Center uses technologies to understand how heritable genetic information of diverse organisms functions in health and disease. Provides research facilities, service cores, and staff for genomics research and training. Core facilities for Bioinformatics,DNA Technologies and Expression Analysis, Metabolomics, Proteomics,TILLING Core,Yeast One Hybrid Services Core. | Heritable, genetic, information, diverse, organism, function, health, disease, core, facility, service, genomic, training, |
is listed by: ScienceExchange is related to: University of California at Davis Genome Center Proteomics Core Facility has parent organization: University of California at Davis; California; USA |
SciEx_227, SciEx_756, SCR_012659 | https://genomecenter.ucdavis.edu/ | http://www.scienceexchange.com/facilities/uc-davis-genome-center-uc-davis | SCR_012480 | University of California Davis Genome Center Labs and Facilities, UC Davis Genome Center Labs & Facilities, University of California Davis Genome Center Labs & Facilities | 2026-02-17 10:02:10 | 1 | ||||||
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SNPFILE Resource Report Resource Website 1+ mentions |
SNPFILE (RRID:SCR_009402) | software library, software application, software resource, software toolkit | Software library and API for manipulating large SNP datasets with associated meta-data, such as marker names, marker locations, individuals'' phenotypes, etc. in an I/O efficient binary file format. In its core, SNPFile assumes very little about the metadata associated with markers and individuals, but leaves this up to application program protocols. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, linux, unix | is listed by: Genetic Analysis Software | nlx_154641 | SCR_009402 | 2026-02-17 10:01:29 | 1 | ||||||||||
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FGED Resource Report Resource Website 10+ mentions |
FGED (RRID:SCR_001897) | FGED | data or information resource, portal, knowledge environment | Society that develop standards for biological research data quality, annotation and exchange. They facilitate the creation and use of software tools that build on these standards and allow researchers to annotate and share their data easily. They promote scientific discovery that is driven by genome wide and other biological research data integration and meta-analysis. Historically, FGED began with a focus on microarrays and gene expression data. However, the scope of FGED now includes data generated using any technology when applied to genome-scale studies of gene expression, binding, modification and other related applications. | gene expression, gene modification, biological, biologist, biomedical, computer scientist, data analyst, genomic, integration, life science, microarray, technology, functional genomics, annotate, data sharing, genome, data integration, software |
is listed by: OMICtools is parent organization of: MINSEQE is parent organization of: MAGE is parent organization of: MIAME |
OMICS_01778, nif-0000-10466 | http://www.mged.org/ | SCR_001897 | Functional Genomics Data Society, MGED Society, The Microarray Gene Expression Data Society, The Functional Genomics Data Society, MGED | 2026-02-17 09:59:47 | 24 | |||||||
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GoMiner Resource Report Resource Website 100+ mentions |
GoMiner (RRID:SCR_002360) | GoMiner | software application, data processing software, software resource | GoMiner is a tool for biological interpretation of "omic" data including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samples, raising the question, What does it all mean biologically? To answer this question, GoMiner leverages the Gene Ontology (GO) to identify the biological processes, functions and components represented in these lists. Instead of analyzing microarray results with a gene-by-gene approach, GoMiner classifies the genes into biologically coherent categories and assesses these categories. The insights gained through GoMiner can generate hypotheses to guide additional research. GoMiner displays the genes within the framework of the Gene Ontology hierarchy in two ways: * In the form of a tree, similar to that in AmiGO * In the form of a "Directed Acyclic Graph" (DAG) The program also provides: * Quantitative and statistical analysis * Seamless integration with important public databases GoMiner uses the databases provided by the GO Consortium. These databases combine information from a number of different consortium participants, include information from many different organisms and data sources, and are referenced using a variety of different gene product identification approaches. | experiment, expression, function, gene, genomics, biological, genomic, microarray, omic, process, gene expression, gene ontology, biological process, biological function, biological component, proteomic, database, FASEB list |
is related to: Gene Ontology is related to: High-Throughput GoMiner has parent organization: Georgia Institute of Technology; Georgia; USA has parent organization: Emory University; Georgia; USA has parent organization: National Cancer Institute |
NCI ; Georgia Institute of Technology; Georgia; USA ; Emory University; Georgia; USA |
PMID:12702209 | nif-0000-21181 | SCR_002360 | 2026-02-17 09:59:55 | 115 | |||||||
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LAPSTRUCT Resource Report Resource Website 1+ mentions |
LAPSTRUCT (RRID:SCR_007550) | software application, software resource | Software application to describe population structure using biomarker data ( typically SNPs, CNVs etc.) available in a population sample. The main features different from PCA are: (1) geometrically motivated and graphic model based; (2)robustness of outliers. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | Free | nlx_154589, SCR_009367, nlx_154209 | SCR_007550 | R/LAPSTRUCT, LAPlacian eigenfunctions learn population STRUCTure | 2026-02-17 10:01:16 | 3 | ||||||||
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Pedigree-Draw Resource Report Resource Website 1+ mentions |
Pedigree-Draw (RRID:SCR_008302) | commercial organization, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Software application for pedigree drawing (entry from Genetic Analysis Software) | gene, genetic, genomic, macos, bio.tools |
is listed by: Genetic Analysis Software is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: OMICtools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154520, OMICS_00213, SCR_010795 | SCR_008302 | PEDIGREE/DRAW | 2026-02-17 10:01:07 | 1 | ||||||||
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Caltech, The Beckman Institute: The Biological Network Modeling Center Resource Report Resource Website 50+ mentions |
Caltech, The Beckman Institute: The Biological Network Modeling Center (RRID:SCR_008060) | data or information resource, portal, organization portal | The Beckman Institute BNMC brings together researchers from many disciplines at Caltech to address problems in the mechanistic modeling of coupled genomic, intercellular and intracellular processes. It represents an attempt to encourage closer interaction and collaboration between groups in Biology, Control and Dynamical Systems, and the Center for Advanced Computing Research. The focus of BNMC is biochemical phenomena occurring within and between cells, in particular the mechanistic modeling of molecular networks of all kinds (e.g., transcriptional, regulatory, metabolic, signal transduction, mechanical, etc.) with and without spatial variation and intercellular communication. BNMC is formed as a coordinated effort aimed at (1) applying existing capabilities to collaboratively solve biological modeling problems that arise in answering scientific questions in Caltech laboratories, (2) exploring a diversity of novel approaches in order to achieve fundamental advances necessary to address the classes of modeling problems biologists want to solve, and (3) organizing projects to better share human experience as well as common infrastructure to avoid duplication and maximize solution interoperability. | dynamical system, advanced computing, biochemical, biological model, biologist, biology, cell, control system, genomic, interaction, intercellular, intercellular communication, intracellular, mechanical, mechanistic modeling, metabolic, regulatory, signal transduction, transcriptional | has parent organization: California Institute of Technology; Pasadena; USA | nif-0000-10444 | SCR_008060 | BNMC | 2026-02-17 10:01:10 | 95 | |||||||||
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NeLS Resource Report Resource Website 1+ mentions |
NeLS (RRID:SCR_016301) | NeLS | data or information resource, portal, organization portal | Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project. | genomic, data, analyze, store, share, archive, electronic, infrastructure, administration, Norway, bio.tools |
is listed by: bio.tools is listed by: Debian |
Research Council of Norway | Free, Freely available | biotools:nels | https://bio.tools/nels https://github.com/elixir-no-nels/nels-core https://bio.tools/nels |
SCR_016301 | Norwegian e-Infrastructure for Life Sciences | 2026-02-17 10:03:00 | 3 | |||||
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PLINK/SEQ Resource Report Resource Website 50+ mentions |
PLINK/SEQ (RRID:SCR_013193) | software library, software application, software resource, software toolkit | An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software) | gene, genetic, genomic, c/c++, r, macos, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: PLINK has parent organization: Harvard University; Cambridge; United States |
Open unspecified license | nlx_154213, biotools:plink-seq | https://bio.tools/plink-seq | SCR_013193 | 2026-02-17 10:01:58 | 77 | ||||||||
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tenx Resource Report Resource Website 10+ mentions |
tenx (RRID:SCR_016957) | production service resource, analysis service resource, service resource, software resource, software toolkit, data analysis service | Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis. | analysis, 10x, single, cell, RNA, sequencing, data, genomic, platform, mapping, quantitation | Free, Available for download, Freely available | SCR_016957 | 2026-02-17 10:03:30 | 11 | |||||||||||
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Kids First Data Resource Portal Resource Report Resource Website 1+ mentions |
Kids First Data Resource Portal (RRID:SCR_016493) | DRP | organization portal, storage service resource, data or information resource, topical portal, disease-related portal, database, service resource, portal, data repository | Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects. | pediatric, genomic, clinical, disease, data, children, cancer, birth, defect, analysis | is recommended by: National Library of Medicine | pediatric cancer, birth defect | the Common Fund’s Gabriella Miller Kids First Pediatric Research Program ; NIH |
Restricted | SCR_016553 | https://commonfund.nih.gov/kidsfirst https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001168.v1.p1 https://commonfund.nih.gov/kidsfirst |
SCR_016493 | Data Resource Portal | 2026-02-17 10:03:02 | 3 | ||||
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OrthoFinder Resource Report Resource Website 1000+ mentions |
OrthoFinder (RRID:SCR_017118) | data analysis software, software application, data processing software, software resource | Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format. | comparative, genomic, analysis, find, orthogroup, ortholog, infer, gene, tree, duplicate, accuracy, protein, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Bill and Melinda Gates Foundation ; UKAID |
PMID:26243257 DOI:10.1101/466201 |
Free, Available for download, Freely available | biotools:OrthoFinder, OMICS_09733, BioTools:OrthoFinder | https://bio.tools/OrthoFinder https://bio.tools/OrthoFinder https://bio.tools/OrthoFinder |
SCR_017118 | OrthoFinder2, OrthoFinder | 2026-02-17 10:03:32 | 2899 | |||||
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ComplexHeatmap Resource Report Resource Website 1000+ mentions |
ComplexHeatmap (RRID:SCR_017270) | software application, data processing software, data analysis software, software resource, data visualization software | Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns. | arrange, multiple, heatmap, visualize, data, pattern, genomic, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools |
German Cancer Research Center-Heidelberg Center for Personalized Oncology ; BMBF |
PMID:27207943 | Free, Available for download, Freely available | biotools:complexheatmap | https://github.com/jokergoo/ComplexHeatmap https://bio.tools/complexheatmap |
SCR_017270 | 2026-02-17 10:03:33 | 3266 | ||||||
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Seurat Resource Report Resource Website 5000+ mentions |
Seurat (RRID:SCR_016341) | software application, data processing software, data analysis software, software resource, software toolkit | Software as R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. | single, cell, genomic, RNA-seq, data, QC, analysis, source, heterogeneity, transcriptomic, measurement, integrate, diverse |
is used by: Stardust is used by: Seurat MapQuery is related to: DoubletFinder is related to: Azimuth works with: SeuratWrappers |
PMID:29608179 | Free, Available for download, Freely available | https://github.com/satijalab/seurat | SCR_016341 | 2026-02-17 10:03:23 | 9395 | ||||||||
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GENERA Resource Report Resource Website 1+ mentions |
GENERA (RRID:SCR_023113) | narrative resource, workflow, data or information resource, training material | Software toolbox to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. | Genomic, Genome assembly, Phylogeny, Phylogenomic, comparative genomic, metabolic analyses, prokaryotes, eukaryotes | Free, Available for download, Freely available | SCR_023113 | GEN-ERA toolbox | 2026-02-17 10:04:22 | 8 |
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