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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 It reports published and unpublished data on human mitochondrial DNA variation.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dna, mutation, phenotype, polymorphism, polypeptide assignment, pseudogene, restriction site, rna, sequence, trna, unpublished, variation, mitochondria, dna, insertion, deletion, FASEB list |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 | SciCrunch Registry | 2026-10-24 12:50:25 | 405 | ||||||
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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 |
NHGRI ; NHLBI U01 HL111561 |
PMID:29140462 | Free, Freely available | nlx_158348 | http://dev3.ccs.miami.edu:8080/datasets-beta/ | http://lifekb.org/ | SCR_003937 | SciCrunch Registry | lifekb, LIFE LINCS Information Framework | 2026-10-24 12:50:27 | 1 | ||||
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PhenoExplorer Resource Report Resource Website |
PhenoExplorer (RRID:SCR_008980) | PhenoExplorer | analysis service resource, data analysis service, production service resource, service resource | A tool for finding dbGaP studies containing phenotype variables of interest. Lack of standardization makes locating and categorizing previously measured variables difficult. This query tool for biomedical researchers is to identify studies and phenotype variables of interest. | phenotype |
is related to: NCBI database of Genotypes and Phenotypes (dbGap) has parent organization: University of Southern California; Los Angeles; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
NHLBI 1UH2HL108780 | Public, Registration required | nlx_152227 | SCR_008980 | SciCrunch Registry | 2026-10-24 12:50:58 | 0 | |||||||
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NHLBI Exome Sequencing Project (ESP) Resource Report Resource Website 1000+ mentions |
NHLBI Exome Sequencing Project (ESP) (RRID:SCR_012761) | EVS | data or information resource, database | The goal of the project is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by pioneering the application of next-generation sequencing of the protein coding regions of the human genome across diverse, richly-phenotyped populations and to share these datasets and findings with the scientific community to extend and enrich the diagnosis, management and treatment of heart, lung and blood disorders. The groups participating and collaborating in the NHLBI GO ESP include: Seattle GO - University of Washington, Seattle, WA Broad GO - Broad Institute of MIT and Harvard, Cambridge, MA WHISP GO - Ohio State University Medical Center, Columbus, OH Lung GO - University of Washington, Seattle, WA WashU GO - Washington University, St. Louis, MO Heart GO - University of Virginia Health System, Charlottesville, VA ChargeS GO - University of Texas Health Sciences Center at Houston | bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
NHLBI | biotools:esp, nlx_156901, biotools:exome_variant_server | https://bio.tools/esp, https://bio.tools/exome_variant_server | SCR_012761 | SciCrunch Registry | Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP) | 2026-10-24 12:51:04 | 2231 | ||||||
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Penn machine learning benchmark repository Resource Report Resource Website |
Penn machine learning benchmark repository (RRID:SCR_017138) | PMLB | data or information resource, data set | Python wrapper for Penn Machine Learning Benchmark data repository. Large, curated repository of benchmark datasets for evaluating supervised machine learning algorithms. Part of PyPI https://pypi.org/ | benchmark, suite, machine, learning, evaluation, comparison, repository, curated, dataset | NCATS TR001263; NEI EY022300; NHLBI HL134015; NIAID AI116794; NIDDK DK112217; NIEHS ES013508; NLM LM009012; NLM LM010098; NLM LM011360; Warren Center for Network and Data Science |
PMID:29238404 | Free, Restricted | https://github.com/EpistasisLab/penn-ml-benchmarks | SCR_017138 | SciCrunch Registry | Penn Machine Learning Benchmark | 2026-10-24 12:52:53 | 0 | ||||||
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ReBATE Resource Report Resource Website |
ReBATE (RRID:SCR_017139) | software resource, software toolkit | 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 | NCATS TR001263; NEI EY022300; NHLBI HL134015; NIAID AI116794; NIDDK DK112217; NIEHS ES013508; NLM LM009012; NLM LM010098; NLM LM011360; Warren Center for Network and Data Science |
PMID:30030120 | Free, Available for download, Freely available | https://epistasislab.github.io/ReBATE/ | SCR_017139 | SciCrunch Registry | Relief Based Algorithm Training Environment | 2026-10-24 12:51:48 | 0 | ||||||
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nbdocker Resource Report Resource Website |
nbdocker (RRID:SCR_017159) | software application, software resource | 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 | Institute of Technology at University of Washington Tacoma ; NHLBI U54 HL127624; NIGMS R01 GM126019 |
DOI:10.1101/309567 | Free, Available for download, Freely available | https://hub.docker.com/r/biodepot/nbdocker/ | SCR_017159 | SciCrunch Registry | 2026-10-24 12:51:48 | 0 | |||||||
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mgatk Resource Report Resource Website 1+ mentions |
mgatk (RRID:SCR_021159) | data processing software, software application, software resource, software toolkit | 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 P01 CA206978; NCI R01 CA208756; NCI U10 CA180861; NHLBI R33 HL120791; NIDDK R01 DK103794 |
DOI:10.1038/s41587-020-0645-6 | Free, Available for download, Freely available | SCR_021159 | SciCrunch Registry | mitochondrial genome analysis toolkit | 2026-10-24 12:50:05 | 4 | ||||||||
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xHLA Resource Report Resource Website 1+ mentions |
xHLA (RRID:SCR_022277) | data processing software, software application, software resource | 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 | Health Resources and Services Administration ; NCI 5U24CA076518; NHLBI 5U10HL069294; Office of Naval Research Grants |
PMID:28674023 | Free, Available for download, Freely available | SCR_022277 | SciCrunch Registry | 2026-10-24 12:50:07 | 2 | |||||||||
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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 | BD2K-LINCS Data Coordination and Integration Center ; NCATS U24TR002278; NHLBI U54HL127624; NLM U01LM012630 |
PMID:31701147 | Free, Freely available | SCR_022566 | SciCrunch Registry | Library of Integrated Network Based Cellular Signatures 2.0 | 2026-10-24 12:50:08 | 2 | ||||||
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Body Mass Index Calculator Resource Report Resource Website |
Body Mass Index Calculator (RRID:SCR_000122) | BMI Calculator | analysis service resource, data analysis service, production service resource, 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 | SciCrunch Registry | Calculate Your Body Mass Index | 2026-10-24 12:50:16 | 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 | SciCrunch Registry | NeuroPedia: Neuropeptide database and spectra library | 2026-10-24 12:50:20 | 12 | |||||
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Drugmonizome Resource Report Resource Website 1+ mentions |
Drugmonizome (RRID:SCR_024821) | data or information resource, database | Database with search engine for querying annotated sets of drugs and small molecules for performing drug set enrichment analysis. | annotated sets of drugs and small molecules, searching of annotated sets of drugs and small molecules, drugs, small molecules, | NCI U24CA224260; NHLBI U54HL127624; NIH Office of the Director OT2OD030160 |
PMID:33787872 | Free, Freely available | SCR_024821 | SciCrunch Registry | 2026-10-24 12:53:24 | 1 | |||||||||
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STARNET Resource Report Resource Website 1+ mentions |
STARNET (RRID:SCR_025238) | STARNET | data access protocol, software resource, source code, web service | Web interactive browser to visualize data and perform gene set enrichment analysis along with gene and SNP lookup. Web interface used to query STARNET datasets and downstream analysis which includes RNAseq from 7 tissues: blood, free internal mammary artery (MAM), atherosclerotic aortic root (AOR), subcutaneous fat (SF), visceral abdominal fat (VAF), skeletal muscle (SKLM), and liver (LIV). Paired SNP genotyping data is included and utilized for tissue expression quantitative trait loci (eQTL), CAD heritability (H2), co-expression networks and gene regulatory networks. | cross-tissue co-expression analysis, STARNET multitissue gene expression data, cardiovascular disease patients, | American Heart Association ; AstraZeneca ; European Union ; Federal German Ministries ; Heart Lung Foundation ; ModulMax ; New South Wales health ; NHLBI HL138193; NHLBI PO1 HL28481; NHLBI R01 HL144651; NHLBI R01 HL147883; NHLBI R01HL125863; NHLBI R01HL130423; NHLBI R01HL135093; NHLBI R01HL148167; NIDDK R01 DK117850; Swedish Research Council |
PMID:36276926 | Free, Freely available | https://github.com/skoplev/starnet | SCR_025238 | SciCrunch Registry | Stockholm-Tartu Atherosclerosis Reverse Networks Engineering Task | 2026-10-24 12:53:34 | 6 | ||||||
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MRQy Resource Report Resource Website 1+ mentions |
MRQy (RRID:SCR_025779) | data analysis software, data processing software, software application, software resource | Software quality assurance and checking tool for quantitative assessment of magnetic resonance imaging and computed tomography data. Used for quality control of MR imaging data. | quantitative assessment, magnetic resonance imaging, computed tomography, imaging data, | NCI 1F31CA216935; NCI 1U01CA239055; NCI 1U01CA248226; NCI R01CA202752; NCI R01CA208236; NCI R01CA216579; NCI R01CA220581; NCI U24CA199374; NCRR 1C06RR12463; NHLBI R01HL15127701A1; NIBIB 1R43EB028736 |
PMID:33176026 | Free, Available for download, Freely available | SCR_025779 | SciCrunch Registry | 2026-10-24 12:53:47 | 1 | |||||||||
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SpaGCN Resource Report Resource Website |
SpaGCN (RRID:SCR_025978) | software application, software resource, source code | Software graph convolutional network to integrate gene expression and histology to identify spatial domains and spatially variable genes. SpaGCN integrates information from gene. | Integrating gene expression and histology, graph convolutional network, identify spatial domains, identify spatially variable genes, | NEI R01EY030192; NEI R01EY031209; NHLBI R01HL113147; NHLBI R01HL150359; NIA P01AG066597; NIGMS R01GM125301 |
PMID:34711970 | Free, Available for download, Freely available | SCR_025978 | SciCrunch Registry | 2026-10-24 12:53:50 | 0 | |||||||||
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Collaborative Cohort of Cohorts for COVID-19 Research Resource Report Resource Website 1+ mentions |
Collaborative Cohort of Cohorts for COVID-19 Research (RRID:SCR_026322) | C4R | data or information resource, disease-related portal, portal, topical portal | Portal provides information about nationwide study of more than 50,000 individuals to determine factors that predict disease severity and long-term health impacts of COVID-19. | nationwide study, determine factors, predict disease severity, long-term health impacts, COVID-19 | COVID-19 | NHLBI ; NIA ; NINDS |
SCR_026322 | SciCrunch Registry | 2026-10-24 12:53:57 | 1 | |||||||||
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Conos Resource Report Resource Website 1+ mentions |
Conos (RRID:SCR_026381) | software resource, software toolkit, source code | Software R package for joint analysis of multiple single-cell RNA-seq datasets. Used to wire together large collections of single-cell RNA-seq datasets, which allows for both identification of recurrent cell clusters and propagation of information between datasets in multi-sample or atlas-scale collections. | joint analysis of multiple single-cell RNA-seq datasets, multiple single-cell RNA-seq datasets, identification of recurrent cell clusters, propagation of information between datasets, multi-sample, atlas-scale collections, | NHLBI R01HL131768; NSF ; Zimin Foundation |
DOI:10.1038/s41592-019-0466-z | Free, Available for download, Freely available | SCR_026381 | SciCrunch Registry | 2026-10-24 12:53:58 | 9 | |||||||||
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Metabolic Subphenotype Predictor Resource Report Resource Website 1+ mentions |
Metabolic Subphenotype Predictor (RRID:SCR_027192) | software resource, source code | Software repository contains code for Inference of T2D metabolic subphenotypes (MuscleIR, Beta-cell Function, Incretin Effect, Hepatic IR), Identification of dominant metabolic subphenotype, Feature extraction from glucose tiemseries, Extraction of reduced representation of glucose tiemseries,Visualization of metabolic phenotypes based on various glucose-related metrics,Concordance between CGM and Venous glucose values from at home and at clinical setting, Classification of metabolic subphenotypes. | Inference of T2D metabolic subphenotypes, identification of dominant metabolic subphenotype, extraction from glucose tiemseries, visualization of metabolic phenotypes, classification of metabolic subphenotype, s | NHLBI 2T32HL09804911; NIDDK R01 DK110186; NIDDK U01 DK085545; NIDDK U01 DK105535; NIDDK UM1DK126185; Stanford Diabetes Research Center ; Stanford PHIND award ; Wellcome Trust |
PMID:39715896 | Free, Available for download, Freely available | SCR_027192 | SciCrunch Registry | 2026-10-24 12:54:15 | 1 | |||||||||
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T Cell ExTRECT Resource Report Resource Website 1+ mentions |
T Cell ExTRECT (RRID:SCR_027742) | software resource, software toolkit, source code | Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes. | T-cell, T cell receptor excision circle, WES data, hg19 or hg38 aligned genomes, | NCATS UL1TR000100; NCI P30CA023100; NCI R21CA177519; NCI U01CA196406; NHLBI U54HL108460; NIH Office of the Director DP5OD017937; NLM T15LM011271; NSF |
PMID:34497419 | Free, Available for download, Freely available | SCR_027742 | SciCrunch Registry | , T cell exome TREC, T cell exome T cell Receptor Excision Circle | 2026-10-24 12:54:27 | 1 |
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