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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Motif Mutation Analysis for Regulatory Genomic Elements Resource Report Resource Website 500+ mentions |
Motif Mutation Analysis for Regulatory Genomic Elements (RRID:SCR_021902) | MMARGE | software application, data processing software, software toolkit, data analysis software, software resource | Software package that integrates genome wide genetic variation with epigenetic data to identify collaborative transcription factor pairs. Optimized to work with chromatin accessibility assays such as ATAC-seq or DNase I hypersensitivity, as well as transcription factor binding data collected by ChIP-seq. Used to identify combinations of cell type specific transcription factors while simultaneously interpreting functional effects of non-coding genetic variation. | genome wide genetic variation, epigenetic data, identify collaborative transcription factor pairs, interpreting functional effects, non-coding genetic variation | NCI CA173903; NIGMS GM085764; NIDDK DK091183; NHLBI R00 123485 |
PMID:29893919 | Free, Available for download, Freely available | SCR_021902 | 2026-02-16 09:50:11 | 608 | ||||||||
|
Atherosclerosis Risk in Communities Resource Report Resource Website 10+ mentions |
Atherosclerosis Risk in Communities (RRID:SCR_021769) | ARIC | data or information resource, topical portal, disease-related portal, portal | Platform for prospective epidemiologic study conducted in four U.S. communities. One of most significant and longest running heart health studies and is the largest study of heart health in African Americans. ARIC investigates risk factors for heart disease and stroke, and connections between cardiovascular and cognitive health. ARIC includes two parts: Cohort Component and Community Surveillance Component. Cohort Component began in 1987, and each ARIC field center randomly selected and recruited cohort sample of individuals aged 45-64 from defined population in their community, to receive extensive examinations, including medical, social, and demographic data. In Community Surveillance Component, four communities are investigated to determine long term trends in hospitalized myocardial infarction and coronary heart disease deaths in men and women aged 35-84 years. | Heart health studies, epidemiologic study, heart disease risk factors, stroke risk factors, cardiovascular and cognitive health connection, atherosclerosis risk | coronary heart disease, stroke, myocardial infarction, atherosclerosis | NHLBI | PMID:2646917 PMID:34112321 |
Free, Freely available | SCR_021769 | The Atherosclerosis Risk in Communities (ARIC) Study | 2026-02-16 09:50:08 | 35 | ||||||
|
MRQy Resource Report Resource Website 1+ mentions |
MRQy (RRID:SCR_025779) | software application, data processing software, data analysis software, 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 U24CA199374; NCI R01CA202752; NCI R01CA208236; NCI R01CA216579; NCI R01CA220581; NCI 1U01CA239055; NCI 1F31CA216935; NCI 1U01CA248226; NHLBI R01HL15127701A1; NIBIB 1R43EB028736; NCRR 1C06RR12463 |
PMID:33176026 | Free, Available for download, Freely available | SCR_025779 | 2026-02-15 09:23:56 | 1 | |||||||||
|
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, topical portal, disease-related portal, 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 ; NINDS ; NIA |
SCR_026322 | 2026-02-15 09:23:14 | 1 | |||||||||
|
Trans-Institute Angiogenesis Research Program Resource Report Resource Website |
Trans-Institute Angiogenesis Research Program (RRID:SCR_000384) | TARP | data or information resource, topical portal, resource, portal | Trans-NIH program encouraging and facilitating the study of the underlying mechanisms controlling blood vessel growth and development. Other aims include: to identify specific targets and to develop therapeutics against pathologic angiogenesis in order to reduce the morbidity due to abnormal blood vessel proliferation in a variety of disease states; to better understand the process of angiogenesis and vascularization to improve states of decreased vascularization; to encourage and facilitate the study of the processes of lymphangiogenesis; and to achieve these goals through a multidisciplinary approach, bringing together investigators with varied backgrounds and varied interests. | blood vessel, growth, development, target, therapeutic, vascularization, angiogenesis, lymphangiogenesis |
is listed by: NIDDK Information Network (dkNET) has parent organization: National Institutes of Health |
Angiogenesis, Lymphangiogenesis | JDRF ; NEI ; NHLBI ; NCI ; NICHD ; NIDDK ; NINDS |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152866 | SCR_000384 | Trans-Institute Angiogenesis Research Program (TARP) | 2026-02-16 09:45:15 | 0 | |||||
|
Cardiovascular Proteomics Center Resource Report Resource Website |
Cardiovascular Proteomics Center (RRID:SCR_000603) | CPC, BUSM CPC | data or information resource, topical portal, portal | The Cardiovascular Proteomics Center is a research center funded by the NIH/NHLBI to analyze and identify proteins that may be modified or created by oxidative stress. The CPC is developing and applying new proteomics methodology and instrumentation to the analysis of known proteins and those yet to be discovered. | protein, cardiovascular, proteomics, heart, oxidative stress, mass spectrometry, biology, clinical | has parent organization: Boston University School of Medicine; Massachusetts; USA | NHLBI N01HV28178-12-0-1 | nlx_149148 | SCR_000603 | BUSM Cardiovascular Proteomics Center, Boston University School of Medicine Cardiovascular Proteomics Center, BU Cardiovascular Proteomics Center | 2026-02-16 09:45:18 | 0 | |||||||
|
YPED Resource Report Resource Website 1+ mentions |
YPED (RRID:SCR_001436) | YPED | data repository, database, storage service resource, service resource, data or information resource | Open source system for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED currently handles LCMS, MudPIT, ICAT, iTRAQ, SILAC, 2D Gel and DIGE. The repository contains data sets which have been released for public viewing and downloading by the responsible Primary Investigators. It includes proteomic data generated by the Yale NIDA Neuroproteomics Center (http://medicine.yale.edu/keck/nida/index.aspx). Sample descriptions are compatible with the evolving MIAPE standards. | proteomics, protein, database, mass spectrometry, neuroscience, data analysis service, small molecule, source code, peptide, protein expression, phosphoprotein, mudpit, dige, icat, itraq |
uses: PANTHER is used by: Integrated Datasets is related to: Integrated Manually Extracted Annotation has parent organization: Yale School of Medicine; Connecticut; USA |
NIDA P30 DA018343; NHLBI N01-HV-28186 |
PMID:17867667 | Free, Freely Available | nlx_152660 | http://medicine.yale.edu/keck/nida/yped.aspx | SCR_001436 | Yale Protein Expression Database | 2026-02-16 09:45:29 | 4 | ||||
|
mgatk Resource Report Resource Website 1+ mentions |
mgatk (RRID:SCR_021159) | data processing software, software application, software toolkit, software resource | 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 | 2026-02-16 09:49:57 | 2 | ||||||||
|
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 | NCI 5U24CA076518; NHLBI 5U10HL069294; Health Resources and Services Administration ; Office of Naval Research Grants |
PMID:28674023 | Free, Available for download, Freely available | SCR_022277 | 2026-02-16 09:50:16 | 2 | |||||||||
|
Body Mass Index Calculator Resource Report Resource Website |
Body Mass Index Calculator (RRID:SCR_000122) | BMI Calculator | production service resource, service resource, data analysis service, analysis 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 | 2026-02-16 09:45:11 | 0 | ||||||
|
PhenoExplorer Resource Report Resource Website |
PhenoExplorer (RRID:SCR_008980) | PhenoExplorer | production service resource, service resource, data analysis service, analysis 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 | 2026-02-16 09:47:19 | 0 | |||||||
|
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 | 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 | 2026-02-16 09:49:10 | 0 | ||||||
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Drugmonizome Resource Report Resource Website 1+ mentions |
Drugmonizome (RRID:SCR_024821) | database, data or information resource | 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 | 2026-02-16 09:50:47 | 1 | |||||||||
|
STARNET Resource Report Resource Website 1+ mentions |
STARNET (RRID:SCR_025238) | STARNET | data access protocol, software resource, web service, source code | 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, | NHLBI R01HL125863; American Heart Association ; Swedish Research Council ; Heart Lung Foundation ; AstraZeneca ; European Union ; Federal German Ministries ; ModulMax ; NHLBI R01HL130423; NHLBI R01HL135093; NHLBI R01HL148167; New South Wales health ; NHLBI R01 HL144651; NHLBI R01 HL147883; NHLBI PO1 HL28481; NIDDK R01 DK117850; NHLBI HL138193 |
PMID:36276926 | Free, Freely available | https://github.com/skoplev/starnet | SCR_025238 | Stockholm-Tartu Atherosclerosis Reverse Networks Engineering Task | 2026-02-16 09:50:54 | 5 | ||||||
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Penn machine learning benchmark repository Resource Report Resource Website |
Penn machine learning benchmark repository (RRID:SCR_017138) | PMLB | data set, data or information resource | 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 | 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:29238404 | Free, Restricted | https://github.com/EpistasisLab/penn-ml-benchmarks | SCR_017138 | Penn Machine Learning Benchmark | 2026-02-16 09:49:10 | 0 | ||||||
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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, | NIGMS R01GM125301; NEI R01EY030192; NEI R01EY031209; NHLBI R01HL113147; NHLBI R01HL150359; NIA P01AG066597 |
PMID:34711970 | Free, Available for download, Freely available | SCR_025978 | 2026-02-16 09:51:03 | 0 | |||||||||
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Conos Resource Report Resource Website 1+ mentions |
Conos (RRID:SCR_026381) | software toolkit, source code, software resource | 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 | 2026-02-16 09:51:09 | 6 | |||||||||
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National Gene Vector Biorepository Resource Report Resource Website 10+ mentions |
National Gene Vector Biorepository (RRID:SCR_004760) | NGVB | service resource, core facility, access service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Archiving services, insertional site analysis, pharmacology and toxicology resources, and reagent repository for academic investigators and others conducting gene therapy research. Databases and educational resources are open to everyone. Other services are limited to gene therapy investigators working in academic or other non-profit organizations. Stores reserve or back-up clinical grade vector and master cell banks. Maintains samples from any gene therapy related Pharmacology or Toxicology study that has been submitted to FDA by U.S. academic investigator that require storage under Good Laboratory Practices. For certain gene therapy clinical trials, FDA has required post-trial monitoring of patients, evaluating clinical samples for evidence of clonal expansion of cells. To help academic investigators comply with this FDA recommendation, the NGVB offers assistance with clonal analysis using LAM-PCR and LM-PCR technology. | gene therapy, clinical trial, testing, insertion site, gene, clinical, vector, cell line, pharmacology, toxicology, clonal analysis, FASEB list |
is related to: NIDDK Information Network (dkNET) is related to: Phoenix has parent organization: Indiana University School of Medicine; Indiana; USA is parent organization of: NGVB SeqMap Database is parent organization of: NGVB Toxicology Database |
NHLBI ; NCRR |
PMID:31910049 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_76398 | http://www.ngvl.org/ https://www.ngvbcc.org/Home.action |
SCR_004760 | 2026-02-16 09:46:24 | 33 | |||||
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iPOP Resource Report Resource Website 10+ mentions |
iPOP (RRID:SCR_008991) | iPOP | data set, data or information resource | Data set generated by personal omics profiling of Dr. Michael Snyder at Stanford University. It combines genomic, transcriptomic, proteomic, metabolomic, and autoantibody profiles from a single individual over a 14 month period. The analysis revealed various medical risks, including type II diabetes. It also uncovered extensive, dynamic changes in diverse molecular components and biological pathways across healthy and diseased conditions. | genomics, proteomics, transcriptional profiling, saliva, blood, maternal data, metabolomics, personalized medicine, adult human, genetics, transcriptome, male | has parent organization: Stanford University; Stanford; California | Healthy | Breetwor Family Foundation ; Korber Foundation ; Fundacion Marcelino Botin ; Fundacion Lilly ; NLM T15-LM007033; NIGMS R24-GM61374; NHLBI T32 HL094274; NHLBI KO8 HL083914; NIH New Investigator DP2 award OD004613; Spanish Ministry of Science and Innovation Projects ; Spanish Ministry of Science and Innovation Projects ; European Union FP7 Genica ; European Union FP7 TELOMARKER ; European Research Council Advanced Grant ; |
PMID:22424236 | Free for personal, Non-exclusive, Non-transferable, Non-commercial access., Please cite. | nlx_152492 | SCR_008991 | Snyderome, Integrated Personal Omics Profiling | 2026-02-16 09:47:19 | 12 | ||||
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T Cell ExTRECT Resource Report Resource Website |
T Cell ExTRECT (RRID:SCR_027742) | software toolkit, source code, software resource | 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, | NHLBI U54HL108460; NCATS UL1TR000100; NCI R21CA177519; NCI P30CA023100; NCI U01CA196406; NLM T15LM011271; NIH Office of the Director DP5OD017937; NSF |
PMID:34497419 | Free, Available for download, Freely available | SCR_027742 | , T cell exome TREC, T cell exome T cell Receptor Excision Circle | 2026-02-16 09:51:28 | 0 |
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