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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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nbdocker Resource Report Resource Website |
nbdocker (RRID:SCR_017159) | software resource, software application | Software tool as Jupyter Notebook extension for Docker. Each Docker container encapsulates its individual computing environment to allow different programming languages and computing environments to be included in one single notebook, provides user to document code as well as computing environment. | Jupyter, notebook, extension, docker, container, code, computing, environment, data | is related to: University of Washington; Seattle; USA | NHLBI U54 HL127624; NIGMS R01 GM126019; Institute of Technology at University of Washington Tacoma |
DOI:10.1101/309567 | Free, Available for download, Freely available | https://hub.docker.com/r/biodepot/nbdocker/ | SCR_017159 | 2026-08-01 12:11:07 | 0 | |||||||
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Nuclear Receptor Signaling Atlas Resource Report Resource Website 100+ mentions |
Nuclear Receptor Signaling Atlas (RRID:SCR_003287) | NURSA | biomaterial supply resource, material resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 25, 2022.Software tool as knowledge environment resource that accrues, develops, and communicates information that advances understanding of structure, function, and role in disease of nuclear receptors (NRs) and coregulators. It specifically seeks to elucidate roles played by NRs and coregulators in metabolism and development of metabolic disorders. Includes large validated data sets, access to reagents, new findings, library of annotated prior publications in field, and journal covering reviews and techniques.As of March 20, 2020, NURSA is succeeded by the Signaling Pathways Project (SPP). | nuclear receptor, coregulator, metabolism, metabolic disorder, type 2 diabetes, obesity, osteoporosis, lipid dysregulation, cardiovascular disease, oncology, regenerative medicine, environmental agent, genomics, proteomics, reagent, ligand, microarray, gene expression, data set, data analysis service, nuclear receptor signaling, signaling, high through put screening, receptor, ligand, journal, molecule, affinity purification, q-pcr, chip-chip, animal model, antibody, cell line, primer, transcriptomine, clinical trial, disease, drug, data set |
is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine lists: NURSA Transcriptomine lists: STRING lists: Nuclear Receptor Cistrome is listed by: NIH Data Sharing Repositories is listed by: NIDDK Research Resources is listed by: NIDDK Information Network (dkNET) is related to: dkCOIN is related to: Integrated Manually Extracted Annotation has parent organization: Baylor College of Medicine; Houston; Texas |
Metabolic disorder, Type 2 diabetes mellitus, Obesity, Osteoporosis, Lipid dysregulation, Cardiovascular disease, Diabetes, Cancer | NHLBI ; NIEHS ; NICHD ; NIDDK DK097748 |
DOI:10.1101/401729 | Free, Freely available | nif-0000-03208 | https://dknet.org/about/NURSA_Archive | http://www.nursa.org | SCR_003287 | NURSA - Nuclear Receptor Signaling Atlas, NURSA - The Nuclear Receptor Signaling Atlas | 2026-08-01 12:10:45 | 135 | ||
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LINCS Data Portal Resource Report Resource Website 10+ mentions |
LINCS Data Portal (RRID:SCR_014939) | data or information resource, portal | Portal which provides a unified interface for searching LINCS dataset packages and reagents. Users can use the portal to access datasets, small molecules, cells, genes, proteins and peptides, and antibodies. | portal, assay, lincs, kinome, dataset, small molecule, cell, gene, protein, peptide, and antibodies. |
is related to: LINCS Data Portal 2.0 has parent organization: University of Miami; Florida; USA is parent organization of: CycIF.org |
NIH Common Fund ; NHLBI 1U01HL111561; NHLBI 3U01HL111561-01S1; NHLBI 3U01HL111561-02S1; NHGRI U54HG006097; NHGRI U54 HG006093 |
Freely available | SCR_014939 | 2026-08-02 09:07:04 | 13 | |||||||||
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HMS LINCS Center Resource Report Resource Website 10+ mentions |
HMS LINCS Center (RRID:SCR_016370) | HMS LINCS | organization portal, data or information resource, portal | Center that is part of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) Program. Its goals are to collect and disseminate data and analytical tools needed to understand how human cells respond to perturbation by drugs, the environment, and mutation. | LINCS, Program, library, network, cell, signature, analysis, drugs, human, research |
is related to: HMS LINCS Database has parent organization: Harvard Medical School; Massachusetts; USA |
NHLBI U54 HL127365 | PMID:29199020 | SCR_016370 | LINCS Center, Harvard Medical School LINCS Center, Harvard Medical School LINCS, Harvard Medical School (HMS) LINCS Center | 2026-08-02 09:07:19 | 15 | |||||||
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LINCS Data Portal 2.0 Resource Report Resource Website 1+ mentions |
LINCS Data Portal 2.0 (RRID:SCR_022566) | LDP v2 | data or information resource, portal | Primary access point for compendium of LINCS data with substantial changes in data architecture and APIs, completely redesigned user interface, and enhanced curated metadata annotations to support more advanced, intuitive and deeper querying, exploration and analysis capabilities. LINCS datasets are accessible at data point level enabling users to directly access and download any subset of signatures across entire library independent from originating source, project or assay. Newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures. | LINCS Data Portal, Cell, molecules, drug | is related to: LINCS Data Portal | NHLBI U54HL127624; BD2K-LINCS Data Coordination and Integration Center ; NCATS U24TR002278; NLM U01LM012630 |
PMID:31701147 | Free, Freely available | SCR_022566 | Library of Integrated Network Based Cellular Signatures 2.0 | 2026-08-02 09:08:32 | 2 | ||||||
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ReBATE Resource Report Resource Website |
ReBATE (RRID:SCR_017139) | software toolkit, software resource | Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity . | compare, relief, feature, algorithm, data, mining, variable, heterogeneous, pattern, genetic | has parent organization: University of Pennsylvania; Philadelphia; USA | NIAID AI116794; NIDDK DK112217; NIEHS ES013508; NEI EY022300; NHLBI HL134015; NLM LM009012; NLM LM010098; NLM LM011360; NCATS TR001263; Warren Center for Network and Data Science |
PMID:30030120 | Free, Available for download, Freely available | https://epistasislab.github.io/ReBATE/ | SCR_017139 | Relief Based Algorithm Training Environment | 2026-08-02 09:07:35 | 0 | ||||||
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Ribosomal Database Project Resource Report Resource Website 1000+ mentions |
Ribosomal Database Project (RRID:SCR_006633) | RDP | resource, data or information resource, database | A database which provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. It specifically contains information on quality-controlled, aligned and annotated bacterial and archaean 16S rRNA sequences, fungal 28S rRNA sequences, and a suite of analysis tools for the scientific community. Most of the RDP tools are now available as open source packages for users to incorporate in their local workflow. | microbiome, database, rrna gene sequence, rrna, ribosome, genome browser, high-throughput sequencing, bacteria, archaea, fungi, FASEB list |
is listed by: OMICtools is listed by: Human Microbiome Project has parent organization: Michigan State University; Michigan; USA is parent organization of: RDPipeline |
DOE DE-FG02-99ER62848; DOE DE-SC0004601; DOE DE-FC02-07ER64494; NIEHS P42 ES004911; NSF DBI-0328255; USDA 2008-35107-04542; NHLBI U01HL098961; NIDDK UH3 DK083993 |
PMID:24288368 PMID:17586664 |
Open source | r3d100012372, nif-0000-03404, OMICS_01513 | https://doi.org/10.17616/R3C087 | SCR_006633 | Ribosomal Database Project | 2026-08-03 09:33:11 | 1441 | ||||
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Human Reference Protein Interactome Project Resource Report Resource Website 10+ mentions |
Human Reference Protein Interactome Project (RRID:SCR_015670) | HuRI | portal, database, web application, data or information resource, software resource, project portal | Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies. | protein interactome, protein-protein interaction, ppi, pairwise combination, proteome, human reference | NHGRI R01/U01HG001715; NHGRI P50HG004233; NHLBI U01HL098166; NHLBI U01HL108630; NCI U54CA112962; NCI R33CA132073; NIH RC4HG006066; NICHD ARRA R01HD065288; NICHD ARRA R21MH104766; NICHD ARRA R01MH105524; NIMH R01MH091350; NSF CCF-1219007; NSERC RGPIN-2014-03892 |
PMID:25416956 | Freely Available, Free, Available for download | SCR_015670 | HuRI: The Human Reference Protein Interactome Mapping Project | 2026-08-03 09:36:22 | 20 | |||||||
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Polysolver Resource Report Resource Website 10+ mentions |
Polysolver (RRID:SCR_022278) | software resource, data processing software, software application, data analysis software | Software tool for HLA typing based on whole exome sequencing data and infers alleles for three major MHC class I genes. Enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using inferred alleles as reference. | HLA typing, whole exome sequencing data, accurate inference of germline alleles, high precision HLA-typing, alleles of class I HLA-A, B and C genes, detection of mutations, inferred alleles | has parent organization: Broad Institute | Blavatnik Family Foundation ; NHLBI 1RO1HL103532; NCI 1R01CA155010; AACR |
PMID:26372948 | Free, Available for download, Freely available | SCR_022278 | POLYmorphic loci reSOLVER, POLYSOLVER | 2026-08-03 09:37:50 | 30 | |||||||
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SigCom LINCS Resource Report Resource Website 1+ mentions |
SigCom LINCS (RRID:SCR_022275) | web service, data access protocol, software resource | Web server that serves over million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. Data and metadata search engine for gene expression signatures. | FAIR data, data and metadata search engine, gene expression signatures, gene expression signature processed, analyzed, and visualized, LINCS, GTEx, GEO, gene expression signatures, | NHLBI U54HL127624; NIDDK R01DK131525; NIH Office of the Director OT2OD030160 |
PMID:35524556 | Free, Freely available | https://github.com/MaayanLab/sigcom-lincs | SCR_022275 | SigCom Library of Integrated Network-based Cellular Signatures | 2026-08-03 09:37:50 | 7 | |||||||
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sei Resource Report Resource Website 1+ mentions |
sei (RRID:SCR_022571) | web service, data access protocol, software resource | Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types. | systematically predicting sequence regulatory activities, applying sequence information, human genetics data, sequence class predictions | National Science Foundation Graduate Research Fellowship Program ; NHGRI R01HG005998; NHLBI U54HL117798; NIGMS R01GM071966 |
PMID:35817977 | Free, Available for download, Freely available | https://hb.flatironinstitute.org/sei | SCR_022571 | 2026-08-03 09:38:02 | 6 | ||||||||
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X2K Web Resource Report Resource Website 10+ mentions |
X2K Web (RRID:SCR_023624) | X2K | web service, data access protocol, software resource | Web service to predict involvement of upstream cell signaling pathways, given signature of differentially expressed genes. Used to linking expression signatures to upstream cell signaling networks. | predicts involvement of upstream cell signaling pathways, differentially expressed genes, linking expression signatures, upstream cell signaling networks, | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | NHLBI U54 HL127624; NCI U24 CA224260; NIH Office of the Director OT3 OD025467 |
PMID:29800326 | Free, Freely available | https://github.com/MaayanLab/x2k_web | SCR_023624 | eXpression2Kinases (X2K) Web | 2026-08-03 09:38:27 | 10 | |||||
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Poly Peak Parser Resource Report Resource Website 1+ mentions |
Poly Peak Parser (RRID:SCR_023776) | web service, data access protocol, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 25,2025. Web tool to parse Sanger sequencing chromatograms with double peaks into wildtype and alternative allele sequences. Used to separate chromatogram data containing ambiguous base calls into wildtype and mutant allele sequences.Used for identification of unknown indels using sanger sequencing of polymerase chain reaction products. | unknown indels identification, parse Sanger sequencing chromatograms, chromatograms with double peaks, separate chromatogram data, ambiguous base calls, wildtype sequences, mutant allele sequences, alternative allele sequences, | NHLBI U01HL0981; NHLBI U01HL098188; NHLBI 1F32HL115881 |
PMID:25160973 | THIS RESOURCE IS NO LONGER IN SERVICE | http://yosttools.genetics.utah.edu/PolyPeakParser/ | SCR_023776 | 2026-08-03 09:38:30 | 5 | ||||||||
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mgatk Resource Report Resource Website 1+ mentions |
mgatk (RRID:SCR_021159) | software toolkit, software resource, software application, data processing software | Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays. | processing .bam files, mitochondrial reads, heteroplasmy estimation, sequencing data, mitochondrial genotypes, mtscATAC-seq | NCI F31 CA232670; NCI R01 CA208756; NCI P01 CA206978; NCI U10 CA180861; NIDDK R01 DK103794; NHLBI R33 HL120791 |
DOI:10.1038/s41587-020-0645-6 | Free, Available for download, Freely available | SCR_021159 | mitochondrial genome analysis toolkit | 2026-08-03 09:37:33 | 2 | ||||||||
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xHLA Resource Report Resource Website 1+ mentions |
xHLA (RRID:SCR_022277) | software resource, software application, data processing software | Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer. | HLA typing, short read sequence data, refines mapping results, amino acid level, four digit typing accuracy | NCI 5U24CA076518; NHLBI 5U10HL069294; Health Resources and Services Administration ; Office of Naval Research Grants |
PMID:28674023 | Free, Available for download, Freely available | SCR_022277 | 2026-08-03 09:37:36 | 2 | |||||||||
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Body Mass Index Calculator Resource Report Resource Website |
Body Mass Index Calculator (RRID:SCR_000122) | BMI Calculator | data analysis service, service resource, analysis service resource, production service resource | Body Mass Index (BMI) for adults can be calculated using only height and weight. Body mass index (BMI) is a measure of body fat based on height and weight that applies to adult men and women. | adult human, body mass, male, female |
is listed by: NIDDK Information Network (dkNET) is listed by: Genetic Analysis Software has parent organization: National Heart Lung and Blood Institute |
NHLBI | Free, Public | nlx_152731 | SCR_000122 | Calculate Your Body Mass Index | 2026-08-03 09:30:58 | 0 | ||||||
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NeuroPedia Resource Report Resource Website 10+ mentions |
NeuroPedia (RRID:SCR_001551) | NeuroPedia | data or information resource, database | A neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species. | proteomics, peptide, neuropeptide, mass spectrometry assay, peptide sequence, spectrum, homolog | has parent organization: Center for Computational Mass Spectrometry | NCRR P41-RR024851; NIDA 5K01DA23065; NINDS R01 NS24553; NIDA R01 DA04271; NIMH R01 MH077305; NHLBI P01 HL58120 |
PMID:21821666 | Free, Freely available | nlx_152894 | SCR_001551 | NeuroPedia: Neuropeptide database and spectra library | 2026-08-03 09:31:26 | 12 | |||||
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UniProt Resource Report Resource Website 10000+ mentions |
UniProt (RRID:SCR_002380) | UniProt | data or information resource, database | Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB. | collection, protein, sequence, annotation, data, functional, information |
is used by: LIPID MAPS Proteome Database is used by: ChannelPedia is used by: Open PHACTS is used by: DisGeNET is used by: Smart Dictionary Lookup is used by: MitoMiner is used by: Cytokine Registry is used by: MobiDB is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: Phospho.ELM is used by: GEROprotectors is used by: SwissLipids is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: LabWorm is related to: Clustal W2 is related to: UniProt DAS is related to: UniParc at the EBI is related to: ProDom is related to: LegumeIP is related to: Pathway Commons is related to: NIH Data Sharing Repositories is related to: FlyMine is related to: IMEx - The International Molecular Exchange Consortium is related to: 3D-Interologs is related to: Biomine is related to: EBIMed is related to: STOP is related to: Coremine Medical is related to: BioExtract is related to: STRAP is related to: GOTaxExplorer is related to: GoAnnotator is related to: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures is related to: Whatizit is related to: MOPED - Model Organism Protein Expression Database is related to: Polbase is related to: PredictSNP is related to: PSICQUIC Registry is related to: IntAct is related to: p300db is related to: UniProt Proteomes is related to: SARS-CoV-2 mutation effects and 3D structure prediction from sequence covariation has parent organization: European Bioinformatics Institute has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: Protein Information Resource is parent organization of: UniProtKB is parent organization of: NEWT is parent organization of: UniParc is parent organization of: UniProt Chordata protein annotation program is parent organization of: UniRef works with: Genotate works with: CellPhoneDB works with: MOLEonline works with: MiMeDB |
NHGRI U41 HG006104; NHGRI P41 HG02273; NIGMS 5R01GM080646; NIGMS R01 GM080646; NLM G08 LM010720; NCRR P20 RR016472; NSF DBI-0850319; British Heart Foundation ; NEI ; NHLBI ; NIA ; NIAID ; NIDDK ; NIMH ; NCI ; EMBL ; PDUK ; ARUK ; NHGRI U24 HG007722 |
PMID:19843607 PMID:18836194 PMID:18045787 PMID:17142230 PMID:16381842 PMID:15608167 PMID:14681372 |
nif-0000-00377, SCR_018750, r3d100010357 | http://www.ebi.uniprot.org, http://www.uniprot.org/uniprot/, http://www.pir.uniprot.org, ftp://ftp.uniprot.org, https://doi.org/10.17616/R3BW2M | SCR_002380 | , The Universal Protein Resource, Universal Protein Resource, UNIPROT Universal Protein Resource | 2026-08-03 09:31:55 | 17565 | |||||
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MITOMAP - A human mitochondrial genome database Resource Report Resource Website 100+ mentions |
MITOMAP - A human mitochondrial genome database (RRID:SCR_002996) | MITOMAP | data or information resource, database | Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf. | gene, genome, diabetes, disease, disease-association, high resolution screening, human, inversion, metabolism, mitochondrial dna, mutation, phenotype, polymorphism, polypeptide assignment, pseudogene, restriction site, rna, sequence, trna, unpublished, variation, mitochondria, dna, insertion, deletion, FASEB list |
is used by: HmtVar is listed by: OMICtools is related to: Hereditary Hearing Loss Homepage has parent organization: Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA has parent organization: Emory University School of Medicine; Atlanta; Georgia; USA |
NIH ; Muscular Dystrophy Foundation ; Ellison Foundation ; Diputacion General de Aragon Grupos consolidados B33 ; NIGMS GM46915; NINDS NS21328; NHLBI HL30164; NIA AG10130; NIA AG13154; NINDS NS213L8; NHLBI HL64017; NIH Biomedical Informatics Training Grant T15 LM007443; NSF EIA-0321390; Spanish Fondo de Investigacion Sanitaria PI050647; Ciber Enfermedades raras CB06/07/0043 |
PMID:17178747 PMID:15608272 PMID:9399813 PMID:9016535 PMID:8594574 |
Except where otherwise noted, Creative Commons Attribution License, The community can contribute to this resource | nif-0000-00511, OMICS_01641 | SCR_002996 | 2026-08-03 09:32:10 | 368 | ||||||
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LINCS Information Framework Resource Report Resource Website 1+ mentions |
LINCS Information Framework (RRID:SCR_003937) | data or information resource, database | LIFE search engine contains data generated from LINCS Pilot Phase, to integrate LINCS content leveraging semantic knowledge model and common LINCS metadata standards. LIFE makes LINCS content discoverable and includes aggregate results linked to Harvard Medical School and Broad Institute and other LINCS centers, who provide more information including experimental conditions and raw data. Please visit LINCS Data Portal. | bioassay, cell, small molecule, kinase protein, compound, cell, gene, metadata standard, cell line, primary cell, rnai reagent, rnai, reagent, protein reagent, protein, antibody reagent, antibody, perturbagen, growth factor, ligand, linked data, organ, disease, data set |
uses: HMS LINCS Database uses: Bioassay Ontology uses: Molecular Libraries Program is related to: Broad Institute is related to: Harvard Medical School; Massachusetts; USA is related to: Columbia University; New York; USA is related to: Yale University; Connecticut; USA is related to: Arizona State University; Arizona; USA has parent organization: University of Miami; Florida; USA |
NHLBI U01 HL111561; NHGRI |
PMID:29140462 | Free, Freely available | nlx_158348 | http://dev3.ccs.miami.edu:8080/datasets-beta/ | http://lifekb.org/ | SCR_003937 | lifekb, LIFE LINCS Information Framework | 2026-08-03 09:32:36 | 1 |
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