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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PLINK/SEQ Resource Report Resource Website 50+ mentions |
PLINK/SEQ (RRID:SCR_013193) | software application, software library, software toolkit, software resource | 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 | 2026-02-15 09:20:25 | 77 | ||||||||
|
Kids First Data Resource Portal Resource Report Resource Website 1+ mentions |
Kids First Data Resource Portal (RRID:SCR_016493) | DRP | organization portal, portal, database, service resource, storage service resource, data repository, data or information resource, topical portal, disease-related portal | 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 | 2026-02-15 09:21:42 | 3 | ||||
|
Seurat Resource Report Resource Website 5000+ mentions |
Seurat (RRID:SCR_016341) | software application, data processing software, software resource, software toolkit, data analysis software | 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 | 2026-02-15 09:21:37 | 9395 | ||||||||
|
tenx Resource Report Resource Website 10+ mentions |
tenx (RRID:SCR_016957) | data analysis service, software resource, service resource, production service resource, analysis service resource, software toolkit | 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 | 2026-02-15 09:21:52 | 11 | |||||||||||
|
OrthoFinder Resource Report Resource Website 1000+ mentions |
OrthoFinder (RRID:SCR_017118) | software application, data processing software, data analysis 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 | 2026-02-15 09:21:56 | 2899 | |||||
|
ComplexHeatmap Resource Report Resource Website 1000+ mentions |
ComplexHeatmap (RRID:SCR_017270) | software application, data visualization software, data processing software, software resource, data analysis 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 | 2026-02-15 09:22:00 | 3266 | ||||||
|
GENERA Resource Report Resource Website 1+ mentions |
GENERA (RRID:SCR_023113) | training material, workflow, data or information resource, narrative resource | 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 | 2026-02-15 09:23:04 | 8 | ||||||||||
|
MADELINE Resource Report Resource Website 1+ mentions |
MADELINE (RRID:SCR_001979) | MADELINE | software application, service resource, software resource | Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review. | gene, genetic, genomic, c, unix, solaris, freebsd, openbsd, macos, ms-windows, cygwin, linux, pedigree, draw, linkage association, family association |
is listed by: OMICtools is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:17488757 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154446, OMICS_00210 | http://eyegene.ophthy.med.umich.edu/#madeline | SCR_001979 | Madeline | 2026-02-15 09:18:13 | 5 | |||||
|
ACGT Inc. Resource Report Resource Website |
ACGT Inc. (RRID:SCR_001026) | ACGT | service resource, analysis service resource, production service resource | Company which provides a suite of molecular biology and genomic services, including DNA sequencing by Sanger and Next Generation Sequencing. All services are offered at a research, GLP or clinical grade levels. | commercial, molecular biology, bioinformatics, genomic, service, dna sequencing | is listed by: ScienceExchange | Restricted | SciEx_10623 | http://www.scienceexchange.com/facilities/acgt-inc | SCR_001026 | 2026-02-15 09:18:02 | 0 | |||||||
|
Ancestrymap Resource Report Resource Website 10+ mentions |
Ancestrymap (RRID:SCR_004353) | ANCESTRYMAP | software application, source code, software resource | Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux. | disease gene, ancestry, gene, genomic, unix, linux, admixture mapping, admixture, genome, linkage disequilibrium, population |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools has parent organization: Harvard Medical School; Massachusetts; USA |
Burroughs Wellcome Fund ; NHGRI K-01 HG002758-01 |
PMID:15088269 | Restricted | nlx_39116, biotools:ancestrymap, OMICS_02083 | https://reich.hms.harvard.edu/software https://bio.tools/ancestrymap |
http://genepath.med.harvard.edu/~reich/Software.htm, http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html | SCR_004353 | 2026-02-15 09:18:45 | 12 | ||||
|
Expression Profiler Resource Report Resource Website 1+ mentions |
Expression Profiler (RRID:SCR_005821) | Expression Profiler | service resource, analysis service resource, data analysis service, production service resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The EP:GO browser is built into EBI's Expression Profiler, a set of tools for clustering, analysis and visualization of gene expression and other genomic data. With it, you can search for GO terms and identify gene associations for a node, with or without associated subnodes, for the organism of your choice. | other analysis, cluster, analysis, visualization, gene expression, genomic, gene ontology, gene association, microarray, protein-protein interaction, gene, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Bioinformatics Institute |
European Union ; Wellcome Trust ; Estonian Science Foundation 5724; Estonian Science Foundation 5722 |
PMID:15215431 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:expression_profiler, nlx_149323 | https://bio.tools/expression_profiler | SCR_005821 | Expression Profiler at the EBI | 2026-02-15 09:19:13 | 6 | ||||
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Mouse Biomedical Informatics Research Network Resource Report Resource Website |
Mouse Biomedical Informatics Research Network (RRID:SCR_003392) | MouseBIRN, mBIRN | atlas, data or information resource, reference atlas, data set | Animal model data primarily focused on mice including high resolution MRI, light and electron microscopic data from normal and genetically modified mice. It also has atlases, and the Mouse BIRN Atlasing Toolkit (MBAT) which provides a 3D visual interface to spatially registered distributed brain data acquired across scales. The goal of the Mouse BIRN is to help scientists utilize model organism databases for analyzing experimental data. Mouse BIRN has ended. The next phase of this project is the Mouse Connectome Project (https://www.nitrc.org/projects/mcp/). The Mouse BIRN testbeds initially focused on mouse models of neurodegenerative diseases. Mouse BIRN testbed partners provide multi-modal, multi-scale reference image data of the mouse brain as well as genetic and genomic information linking genotype and brain phenotype. Researchers across six groups are pooling and analyzing multi-scale structural and functional data and integrating it with genomic and gene expression data acquired from the mouse brain. These correlated multi-scale analyses of data are providing a comprehensive basis upon which to interpret signals from the whole brain relative to the tissue and cellular alterations characteristic of the modeled disorder. BIRN's infrastructure is providing the collaborative tools to enable researchers with unique expertise and knowledge of the mouse an opportunity to work together on research relevant to pre-clinical mouse models of neurological disease. The Mouse BIRN also maintains a collaborative Web Wiki, which contains announcements, an FAQ, and much more. | electron microscopy, expression, functional, gene, 3-dimentional, brain, cellular, disorder, genomic, genotype, mouse, neurodegenerative disease, phenotype, molecular neuroanatomy resource, mri, light microscopy, model organism, gene expression, atlas data, imaging genomics, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Mouse BIRN Atlasing Toolkit is related to: Mouse Connectome Project has parent organization: Biomedical Informatics Research Network |
Normal, Neurodegenerative disease, Multiple Sclerosis, Alzheimer's disease, Parkinson's disease | NIH ; Collaborative Tools Support Network Award ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01 |
Free, Available for download, Freely available | nif-0000-00200 | https://loni.usc.edu/research/software?name=MBATWA | http://www.loni.ucla.edu/BIRN/Projects/Mouse/index.shtml | SCR_003392 | Mouse BIRN | 2026-02-15 09:18:30 | 0 | |||
|
AirPROM Resource Report Resource Website |
AirPROM (RRID:SCR_003827) | AirPROM | organization portal, data or information resource, consortium, portal | Consortium focused on developing computer and physical models of the airway system for patients with asthma and chronic obstructive pulmonary disease (COPD). Developing accurate models will better predict how asthma and COPD develop, since current methods can only assess the severity of disease. They aim to bridge the gaps in clinical management of airways-based disease by providing reliable models that predict disease progression and the response to treatment for each person with asthma or COPD. A data management platform provides a secure and sustainable infrastructure that semantically integrates the clinical, physiological, genetic, and experimental data produced with existing biomedical knowledge from allied consortia and public databases. This resource will be available for analysis and modeling, and will facilitate sharing, collaboration and publication within AirPROM and with the broader community. Currently the AirPROM knowledge portal is only accessible by AirPROM partners. | model, airway system, lung, consortium, clinical, imaging, respiratory system, tissue sample, airway model, genomic, gas diffusion mri, airway development, function, physiological, genetic, computational model, gene-environment interaction |
is listed by: Consortia-pedia has parent organization: European Lung Foundation |
European Union FP7 | nlx_158142 | SCR_003827 | Airway Disease Predicting Outcomes through Patient Specific Computational Modelling | 2026-02-15 09:18:35 | 0 | |||||||
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Cohorts for Heart and Aging Research in Genomic Epidemiology Resource Report Resource Website 10+ mentions |
Cohorts for Heart and Aging Research in Genomic Epidemiology (RRID:SCR_004034) | CHARGE Consortium, CHARGE | organization portal, portal, consortium, data or information resource, bibliography | Consortium formed to facilitate genome-wide association study meta-analyses and replication opportunities among multiple large and well-phenotyped longitudinal cohort studies. A bibliography of CHARGE publications is available. Its founding member cohorts include: * Age, Gene, Environment, Susceptibility Study -- Reykjavik * Atherosclerosis Risk in Communities Study * Cardiovascular Health Study * Framingham Heart Study * Rotterdam Study Additional core cohorts include: * Coronary Artery Risk Development in Young Adults * Family Heart Study * Health, Aging, and Body Composition Study * Jackson Heart Study * Multi-Ethnic Study of Atherosclerosis | genome-wide association study, genomic, epidemiology, phenotype, longitudinal | is related to: International Genomics of Alzheimers Project | Aging, Heart disease | PMID:20031568 | nlx_158460 | SCR_004034 | 2026-02-15 09:18:37 | 17 | |||||||
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NeMOarchive Resource Report Resource Website 100+ mentions |
NeMOarchive (RRID:SCR_016152) | NeMO | database, service resource, storage service resource, data repository, data or information resource | Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility. | omic, neuroscience, neurobiology, bcbc, biccn, nih, brain, genomic, region, abnormal, transcription, factor, binding, site, chromatin, regulatory, element, data |
is used by: BRAIN Initiative Cell Atlas Network is used by: BICCN is recommended by: BRAIN Initiative is related to: NeMO Analytics has parent organization: University of Maryland School of Medicine; Maryland; USA |
NIMH MH114788; BRAIN Initiative |
Free, Freely available | https://data.nemoarchive.org/ | SCR_016152 | NeMO Archive, Neuroscience Multi-omic Data Archive, The Neuroscience Multi-Omic Archive, Neuroscience Multi-Omic Archive | 2026-02-15 09:21:02 | 113 | ||||||
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DISULFIND Resource Report Resource Website 50+ mentions |
DISULFIND (RRID:SCR_016072) | Disulfinder | software application, sequence analysis software, data processing software, software resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks. | predict, disulfide, bonding, state, cysteine, protein, sequence, genomic, annotation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: University of Florence; Florence; Italy |
EU STREP APrIL II contract no. FP6-508861; EU NoE BIOPATTERN contract no. FP6-508803; Embark Fellowship from the Irish Research Council for Science ; Engineering and Technology |
PMID:16844986 DOI:10.1093/nar/gkl266 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04214, biotools:disulfind | https://bio.tools/disulfind https://sources.debian.org/src/disulfinder/ |
SCR_016072 | Cysteines Disulfide Bonding State and Connectivity Predictor | 2026-02-15 09:21:01 | 66 | ||||
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Gff2aplot Resource Report Resource Website |
Gff2aplot (RRID:SCR_016128) | software application, data visualization software, data processing software, software resource | Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis. | alignment, pair-wise, plot, genomic, sequence, visualize, together, annotate, analysis, parameter, dataset, |
is listed by: Debian is listed by: OMICtools |
PMID:14668236 | Free, Available for download | OMICS_19949 | https://sources.debian.org/src/gff2aplot/ | SCR_016128 | 2026-02-15 09:21:48 | 0 | |||||||
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Ximmer Resource Report Resource Website 1+ mentions |
Ximmer (RRID:SCR_016427) | software application, data visualization software, data processing software, software resource, simulation software, data analysis software | Software to help users of targeted high throughput genomic sequencing data to accurately detect copy number variants (CNVs). Framework for running and evaluating other copy number detection tools.Used for evaluating and improving performance of CNV detection in exome and targeted sequencing data. | cnv, copy, number, variant, exome, targeted, sequencing, data, next, generation, genomic | is listed by: OMICtools | National Human Genome Research Institute ; National Eye Institute ; National Heart Lung and Blood Institute ; Australian National Health and Medical Research Council ; Victorian State Government |
DOI:10.1101/260927 | Open source, Free, Available for download, Freely available | https://omictools.com/ximmer-tool http://ximmer.org |
SCR_016427 | 2026-02-15 09:21:52 | 4 | |||||||
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GOTrack Resource Report Resource Website 1+ mentions |
GOTrack (RRID:SCR_016399) | database, software resource, data access protocol, web service, data or information resource | Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis. | database, system, access, historical, monitor, record, gene, genomic, data, analysis, ontology, annotation, bioinformatics |
is listed by: OMICtools is related to: University of British Columbia; British Columbia; Canada |
NIH MH111099; NSERC Discovery Grant ; Canadian Foundation for Innovation infrastructure ; CIHR |
DOI:10.1101/320861 | Free, Available for download, Freely available | https://github.com/PavlidisLab/gotrack https://omictools.com/gotrack-tool |
SCR_016399 | 2026-02-15 09:21:05 | 1 | |||||||
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CajaDB Resource Report Resource Website 1+ mentions |
CajaDB (RRID:SCR_016506) | web application, data or information resource, database, software resource | Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network. | marmoset, data, genomic, expression, alternative, splicing, animal, model, neuropsychiatry, social, behavior, ontology, protein, network | Amazonas State Research Support Foundation ; Federal University of Rio Grande do Norte ; Brain Institute ; Multidisciplinary Environment ; NPAD/UFRN ; Brazilian Council for Research and Technological Development |
Free, Freely available | SCR_016506 | 2026-02-15 09:21:42 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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