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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Appyters Resource Report Resource Website 1+ 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 | 2026-02-14 02:04:12 | 9 | |||||||
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Atherosclerosis Risk in Communities Resource Report Resource Website 10+ mentions |
Atherosclerosis Risk in Communities (RRID:SCR_021769) | ARIC | disease-related portal, data or information resource, 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 | 2026-02-14 02:04:21 | 35 | ||||||
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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 processing software, data analysis software, software toolkit, software application, 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 | 2026-02-14 02:04:24 | 608 | ||||||||
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Polysolver Resource Report Resource Website 10+ mentions |
Polysolver (RRID:SCR_022278) | data analysis software, software resource, data processing software, software application | 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 | 2026-02-14 02:04:42 | 30 | |||||||
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SigCom LINCS Resource Report Resource Website 1+ mentions |
SigCom LINCS (RRID:SCR_022275) | data access protocol, software resource, web service | 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 | 2026-02-14 02:04:38 | 7 | |||||||
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sei Resource Report Resource Website 1+ mentions |
sei (RRID:SCR_022571) | data access protocol, software resource, web service | 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 | 2026-02-14 02:05:02 | 6 | ||||||||
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Sleep Heart Health Study Resource Report Resource Website 50+ mentions |
Sleep Heart Health Study (RRID:SCR_016559) | SHHS | disease-related portal, data or information resource, portal, topical portal | Portal for a multi-cohort study focused on sleep-disordered breathing and cardiovascular outcomes implemented by the National Heart Lung and Blood Institute. Recorded signals are: EEG, ECG, EOG, SaO2, HR, EOG, EMG, respiratory inductance plethysmography, respiration (thermistor), position, light. | dataset, analysis, sleep, apnea, breathing, disorder, cardiovascular, disease, EEG, ECG, respiration, PSG | is listed by: National Sleep Research Resource (NSRR) | sleep disorder, sleep apnea, cardiovascular disease | NHLBI U01 HL53916; NHLBI U01 HL53931; NHLBI U01 HL53934; NHLBI U01 HL53937; NHLBI U01 HL64360; NHLBI U01 HL53938; NHLBI U01 HL53941 |
PMID:9493915 | Free, Freely available, Registration required for membership | SCR_016559 | Sleep Heart Health Study | 2026-02-14 02:03:14 | 76 | |||||
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SINCERA Pipeline Resource Report Resource Website 1+ mentions |
SINCERA Pipeline (RRID:SCR_016563) | SINCERA | data processing software, data analysis software, data analytics software, software application, software resource | Software tool implemented in R S4 as an analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. Used for Single Cell RNA-Seq profiling analysis. | single, cell, RNA seq, data, sorted, whole, organ, profiling, analysis | NHLBI U01 HL110964; NHLBI U01 HL122642; NHLBI R01 HL105433 |
PMID:26600239 | Free, Available for download, Freely available | https://research.cchmc.org/pbge/sincera.html | SCR_016563 | SINCERA, SINgle CEll RNA seq profiling Analysis | 2026-02-14 02:03:14 | 5 | ||||||
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Drug Gene Budger Resource Report Resource Website |
Drug Gene Budger (RRID:SCR_016489) | DGB | data access protocol, software resource, web service, service resource | Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures. | identify, drug, small, molecule, predict, influence, expression, mammalian, gene, regulate, target |
is related to: LINCS Project has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA works with: CMAP works with: Gene Expression Omnibus (GEO) |
BD2K-LINCS Data Coordination and Integration Center Mount Sinai Knowledge Management Center for IDG ; NHLBI U54 HL127624; NCI U24 CA224260 |
PMID:30169739 | Restricted | SCR_016489 | Drug Gene Budger | 2026-02-14 02:03:05 | 0 | ||||||
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Apnea, Bariatric surgery, and CPAP study Resource Report Resource Website |
Apnea, Bariatric surgery, and CPAP study (RRID:SCR_016575) | ABC study | disease-related portal, data or information resource, portal, topical portal | Portal for randomized controlled trial to compare effectiveness of bariatric surgery versus continuous positive airway pressure (CPAP) therapy for obstructive sleep apnea. Signals included in the polysomnography (PSG) montage are EEG, EMG, EOG, ECG, SpO2, airflow, CPAP pressure, CPAP flow, plethysmography, position, pulse, light, respiratory effort, snore. | dataset, bariatric, surgery, continuous, positive, airway, pressure, therapy, sleep, apnea, obesity II | is listed by: National Sleep Research Resource (NSRR) | class II obesity, obstructive sleep apnea | NHLBI R01 HL106410; NHLBI K24 HL127307 |
DOI:10.1164/rccm.201708-1637LE | Free, Available for public download, Registration required | SCR_016575 | and Cpap study, Bariatric surgery, Apnea | 2026-02-14 02:03:06 | 0 | |||||
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Best Apnea Interventions for Research (BestAIR) sleep study Resource Report Resource Website 1+ mentions |
Best Apnea Interventions for Research (BestAIR) sleep study (RRID:SCR_016583) | BestAIR | disease-related portal, data or information resource, portal, topical portal | Portal for sleep study to address challenges in conducting future large-scale trials of sleep apnea treatment. Includes data from sleep apnea patients with cardiovascular disease or risk factors. Signals included in the polysomnography (PSG) montage are ECG, SpO2, airflow, nasal pressure, position, pulse, respiratory effort, snore, tidal volume. | data, analysis, sleep, apnea, treatment, cardiovascular, disease, risk, factor, polysomnography, ECG, SpO2 | is listed by: National Sleep Research Resource (NSRR) | sleep apnea, cardiovascular disease | ResMed Foundation ; Philips Respironics ; NHLBI U34 HL105277 |
DOI:10.5665/sleep.4266 | SCR_016583 | bestair, , Best Apnea Interventions for Research, Bestair | 2026-02-14 02:03:17 | 2 | ||||||
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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 | 2026-02-14 02:05:13 | 13 | |||||||||
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HMS LINCS Center Resource Report Resource Website 10+ mentions |
HMS LINCS Center (RRID:SCR_016370) | HMS LINCS | data or information resource, organization portal, 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 | 2026-02-14 02:05:40 | 15 | |||||||
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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 | 2026-02-14 02:06:16 | 1 | ||||
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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 U01HL0981; NHLBI U01HL098188; NHLBI 1F32HL115881 |
PMID:25160973 | THIS RESOURCE IS NO LONGER IN SERVICE | http://yosttools.genetics.utah.edu/PolyPeakParser/ | SCR_023776 | 2026-02-14 02:05:00 | 5 | ||||||||
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Body Mass Index Calculator Resource Report Resource Website |
Body Mass Index Calculator (RRID:SCR_000122) | BMI Calculator | data analysis service, production service resource, service resource, 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 | 2026-02-14 02:05:31 | 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 | 2026-02-14 02:05:35 | 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 | 2026-02-14 02:05:47 | 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 | 2026-02-14 02:05:42 | 368 | ||||||
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mgatk Resource Report Resource Website 1+ mentions |
mgatk (RRID:SCR_021159) | data processing software, software resource, software toolkit, software application | 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 | 2026-02-14 02:05:42 | 2 |
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