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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-02-12 09:46:05 | 13 | |||||||||
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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 | 2026-02-12 09:47:25 | 2 | ||||||
|
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 | 2026-02-12 09:47:45 | 9 | |||||||
|
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 | 2026-02-13 10:58:35 | 35 | ||||||
|
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 | 2026-02-13 10:58:40 | 608 | ||||||||
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CycIF.org Resource Report Resource Website 10+ mentions |
CycIF.org (RRID:SCR_016267) | CycIF.org | immuno detection protocol, experimental protocol, data or information resource, immunofluorescence, narrative resource, web page | Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence. | immunofluorescence, cyclic, cycif, data, software, single cell, numeric, dataset, intratumoural, heterogeneity | has parent organization: LINCS Data Portal | NHLBI U54 HL127365 | PMID:26399630 | Public | SCR_016267 | cycif.org | 2026-02-13 10:57:43 | 13 | ||||||
|
star-for-criu Resource Report Resource Website 1+ mentions |
star-for-criu (RRID:SCR_016294) | data processing software, alignment software, software application, software resource, image analysis software | Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability. | hot, start, container, star, aligner, sequencing, data, processing, biomedical, cloud, reproducibility, RNA, analysis, computing, environment | is related to: Systems Transcriptional Activity Reconstruction | NHLBI U54 HL127624; AMEDD Advanced Medical Technology Initiative ; NIGMS R01 GM126019 |
Free, Freely available, Available for download | https://github.com/paizhang/Hotstarting-For-STAR-Alignment | SCR_016294 | 2026-02-13 10:57:47 | 1 | ||||||||
|
LINCS Joint Project - Breast Cancer Network Browser Resource Report Resource Website 1+ mentions |
LINCS Joint Project - Breast Cancer Network Browser (RRID:SCR_016181) | LJP-BCNB, LJP, BCNB | data access protocol, software resource, web service, service resource | Interactive on line tool where signatures are tagged with user selected metadata and external transcript signatures are projected onto network. Browser to visualize signatures from breast cancer cell lines treated with single molecule perturbations. | breast, cancer, tissue, cluster, drug, perturbation, cell, line, gene, expression |
is related to: L1000 Characteristic Direction Signature Search Engine is related to: LINCS Project |
Breast cancer | NHLBI U54 HL127624; NHLBI U54 HL127365; NHGRI U54 HG006093; NCI U54 CA189201 |
PMID:29084964 | Free, Freely available | https://github.com/MaayanLab/LJP | SCR_016181 | LINCS Joint Project, Breast Cancer Network Browser | 2026-02-13 10:57:44 | 1 | ||||
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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 | 2026-02-13 10:57:47 | 0 | ||||||
|
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 | 2026-02-13 10:57:48 | 76 | |||||
|
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 | 2026-02-13 10:57:48 | 5 | ||||||
|
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 | 2026-02-13 10:57:48 | 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 | 2026-02-13 10:57:50 | 2 | ||||||
|
TopDom Resource Report Resource Website 10+ mentions |
TopDom (RRID:SCR_016964) | TOPDOM | data processing software, data analysis software, software toolkit, software application, software resource | Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | identify, topological, domain, genome, structure, linear, time, data, analysis |
has parent organization: University of Southern California; Los Angeles; USA works with: CCTOP |
NHLBI U01 HL108634; NIDDK U54 DK107981; NSF CAREER 0747475; NSF CAREER 1150287; Arnold and Mabel Beckman foundation ; Pew Charitable Trusts |
PMID:26704975 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016964 | TOPological DOMains, Topological Domains, TopDom_v0.0.2, TopDom_v0.0.1 | 2026-02-13 10:57:49 | 10 | ||||||
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Lifestyle Interventions for Expectant Moms (LIFE-Moms) Resource Report Resource Website |
Lifestyle Interventions for Expectant Moms (LIFE-Moms) (RRID:SCR_014376) | LIFE-Moms | data or information resource, organization portal, portal, resource | A consortium whose overall goal is to identify effective behavioral and lifestyle interventions that will improve weight, glycemic control and other pregnancy-related outcomes in obese and overweight pregnant women, and determine whether these interventions reduce obesity and metabolic abnormalities in their children. The study/consortium is comprised of seven clinical centers, with each clinical center conducting its own trial. Additional information on the consortium and individual trials is located in the Consortium Summaries tab. | pregnant, pregnancy, obesity, metabolic abnormality, behavioral intervention, lifestyle intervention, clinical trial |
is listed by: NIDDK Information Network (dkNET) is listed by: NIDDK Research Resources |
Obesity | NIDDK ; NHLBI ; NICHD ; National Center for Complementary and Integrative Health ; Office of Research on Womens Health ; Office of Behavioral and Social Sciences Research |
Synopses available, Users may access trial data at clinicaltrial.gov | http://www.niddk.nih.gov/research-funding/research-resources/Pages/default.aspx | SCR_014376 | Lifestyle Interventions for Expectant Moms | 2026-02-13 10:57:18 | 0 | |||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | web service, analysis service resource, production service resource, service resource, data access protocol, software resource | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NHLBI U54 HL127624; NIEHS P30 ES006096; NIMH R01 MH107487; NCI T32 CA236764; NCATS UL1 TR001425; NIGMS U01 GM120953 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-02-13 10:58:22 | 4 | ||||||||
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variancePartition Resource Report Resource Website 50+ mentions |
variancePartition (RRID:SCR_019204) | data processing software, data analysis software, data analytics software, software application, software resource | Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays. | Repeated measures, variation in gene expression, RNA-seq datasets, high throughput genomic assays, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays, epigenomic sequencing assays, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: CRAN |
NHLBI U01 HL107388; Icahn School of Medicine at Mount Sinai |
PMID:27884101 | Free, Available for download, Freely available | biotools:variancepartition | https://bio.tools/variancepartition | SCR_019204 | 2026-02-13 10:58:25 | 52 | ||||||
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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 | 2026-02-13 10:57:48 | 15 | |||||||
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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 | 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 | 2026-02-13 10:59:00 | 10 | |||||
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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 | 2026-02-13 10:59:05 | 5 |
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