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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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X2K Web Resource Report Resource Website 10+ mentions |
X2K Web (RRID:SCR_023624) | X2K | data access protocol, software resource, web service | 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 | NCI U24 CA224260; NHLBI U54 HL127624; NIH Office of the Director OT3 OD025467 |
PMID:29800326 | Free, Freely available | https://github.com/MaayanLab/x2k_web | SCR_023624 | eXpression2Kinases (X2K) Web | 2026-08-29 11:28:28 | 25 | |||||
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Poly Peak Parser Resource Report Resource Website 1+ mentions |
Poly Peak Parser (RRID:SCR_023776) | data access protocol, software resource, web service | 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 1F32HL115881; NHLBI U01HL0981; NHLBI U01HL098188 |
PMID:25160973 | THIS RESOURCE IS NO LONGER IN SERVICE | http://yosttools.genetics.utah.edu/PolyPeakParser/ | SCR_023776 | 2026-08-29 11:28:03 | 5 | ||||||||
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Appyters Resource Report Resource Website 10+ mentions |
Appyters (RRID:SCR_021245) | software resource, web application | Collection of web-based software applications that enable users to execute bioinformatics workflows without coding. Turns Jupyter notebooks into fully functional standalone web-based bioinformatics applications. Each Appyter application introduces data entry form for uploading or fetching data, as well as for selecting options for various settings. Once user presses Submit, Appyter is executed in cloud and user is presented with Jupyter Notebook report that contain results. Report includes markdown text, interactive and static figures, and source code. Appyter users can share the link to the output report, as well as download the fully executable notebook for execution on other platforms. | Jupyter Notebooks, data-driven web apps collection, Jupyter Notebook results report |
is used by: Hypothesis Center has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U24 CA224260; NHLBI U54 HL127624; NIH Office of the Director OT2 OD030160 |
DOI:10.1016/j.patter.2021.100213 | Free, Available for download, Freely available | https://github.com/MaayanLab/appyter, https://github.com/MaayanLab/appyter-catalog | SCR_021245 | 2026-08-29 11:27:14 | 16 | |||||||
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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 | lifekb, LIFE LINCS Information Framework | 2026-08-29 11:29:23 | 1 | ||||
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iPOP Resource Report Resource Website 10+ mentions |
iPOP (RRID:SCR_008991) | iPOP | data or information resource, data set | 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 | 2026-08-29 11:31:55 | 14 | ||||
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ACCORD Resource Report Resource Website 100+ mentions |
ACCORD (RRID:SCR_009015) | ACCORD | clinical trial, resource | Study testing whether strict glucose control lowers the risk of heart disease and stroke in adults with type 2 diabetes. In addition the study is exploring: 1) Whether in the context of good glycemic control the use of different lowering lipid drugs will further improve these outcomes and 2) If strict control of blood pressure will also have additional beneficial effects on reducing cardiovascular disease. The design was a randomized, multicenter, double 2 X 2 factorial trial in 10,251 patients with type 2 diabetes mellitus. It was designed to test the effects on major CVD events of intensive glycemia control, of fibrate treatment to increase HDL-cholesterol and lower triglycerides (in the context of good LDL-C and glycemia control), and of intensive blood pressure control (in the context of good glycemia control), each compared to an appropriate control. All 10,251 participants were in an overarching glycemia trial. In addition, one 2 X 2 trial addressed the lipid question in 5,518 of the participants and the other 2 X 2 trial addressed the blood pressure question in 4,733 of the participants. The glycemia trial was terminated early due to higher mortality in the intensive compared with the standard glycemia treatment strategies. The results were published in June 2008 (N Eng J Med 2008;358:2545-59). Study-delivered treatment for all ACCORD participants was stopped on June 30, 2009, and the participants were assisted as needed in transferring their care to a personal physician. The lipid and blood pressure results (as well as the microvascular outcomes and eye substudy results) were published in 2010. All participants are continuing to be followed in a non-treatment observational study. | middle adult human, late adult human, glycemic control, lowering lipid drug, blood pressure, lipid, clinical |
is related to: NIDDK Information Network (dkNET) has parent organization: National Heart Lung and Blood Institute |
Cardiovascular disease, Stroke, Type 2 diabetes, Diabetes, Aging | NHLBI ; NIDDK ; NEI ; CDC ; NIA |
PMID:23490598 PMID:23253271 PMID:23238658 PMID:22723583 PMID:22646230 |
nlx_152746 | SCR_009015 | Action to Control Cardiovascular Disease Risk in Diabetes | 2026-08-29 11:31:59 | 180 | |||||
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National Gene Vector Biorepository Resource Report Resource Website 10+ mentions |
National Gene Vector Biorepository (RRID:SCR_004760) | NGVB | access service resource, core facility, 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 |
NCRR ; NHLBI |
PMID:31910049 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_76398 | http://www.ngvl.org/, https://www.ngvbcc.org/Home.action | SCR_004760 | 2026-08-29 11:31:59 | 33 | |||||
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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 | 2026-08-29 11:33:44 | 1 | |||||||||
|
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 | Penn Machine Learning Benchmark | 2026-08-29 11:33:15 | 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 | Relief Based Algorithm Training Environment | 2026-08-29 11:31:21 | 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 | 2026-08-29 11:31:13 | 0 | |||||||
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Atherosclerosis Risk in Communities Resource Report Resource Website 10+ mentions |
Atherosclerosis Risk in Communities (RRID:SCR_021769) | ARIC | data or information resource, disease-related portal, portal, topical 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 | 2026-08-29 11:27:16 | 43 | ||||||
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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 | data analysis software, data processing software, software application, software resource, software toolkit | 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; NHLBI R00 123485; NIDDK DK091183; NIGMS GM085764 |
PMID:29893919 | Free, Available for download, Freely available | SCR_021902 | 2026-08-29 11:27:20 | 608 | ||||||||
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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 | Stockholm-Tartu Atherosclerosis Reverse Networks Engineering Task | 2026-08-29 11:34:00 | 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 | 2026-08-29 11:34:12 | 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 | 2026-08-29 11:34:16 | 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 | 2026-08-29 11:34:42 | 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 | 2026-08-29 11:34:27 | 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 | 2026-08-29 11:35:09 | 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 | , T cell exome TREC, T cell exome T cell Receptor Excision Circle | 2026-08-29 11:35:30 | 1 |
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