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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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L1000 Characteristic Direction Signature Search Engine Resource Report Resource Website 1+ mentions |
L1000 Characteristic Direction Signature Search Engine (RRID:SCR_016177) | L1000CDS2 | service resource, data set, data or information resource, database, data access protocol, software resource, web service | LINCS L1000 characteristic direction signatures search engine. Software tool to find consensus signatures that match user’s input gene lists or input signatures. Underlying dataset is LINCS L1000 small molecule expression profiles generated at Broad Institute by Connectivity Map team. Differentially expressed genes of these profiles were calculated using multivariate method called Characteristic Direction. | signature, gene, dataset, ligand, characteristic, expression, benchmark |
is related to: LINCS Joint Project - Breast Cancer Network Browser has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NHLBI U54 HL127624; NCI U54 CA189201 |
PMID:28413689 | Free, Freely available | SCR_016177 | 2026-07-28 09:44:14 | 8 | |||||||
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Harmonizome Resource Report Resource Website 100+ mentions |
Harmonizome (RRID:SCR_016176) | software application, web application, data or information resource, database, software resource, data processing software, data visualization software | Web application that allows for searching, visualization, and prediction about genes and proteins. It contains a collection of processed datasets gathered to serve and mine knowledge about genes and proteins from major online resources. | gene, protein, visualization, search, prediction, functional | BD2K-LINCS Data Coordination and Integration Center ; Illuminating the Druggable Genome ; Knowledge Management Center ; NIGMS R01 GM098316; NHLBI U54 HL127624; NCI U54 CA189201 |
PMID:27374120 | Freely available, Free, Available for download | SCR_016176 | 2026-07-28 09:44:11 | 127 | |||||||||
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caHUB Resource Report Resource Website |
caHUB (RRID:SCR_009657) | caHUB | data or information resource, narrative resource, standard specification | THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. A national center for biospecimen science and standards to advance cancer research and treatment. It was created in response to the critical and growing need for high-quality, well-documented biospecimens for cancer research. The initiative builds on resources already developed by the NCI, including the Biospecimen Research Network and the NCI Best Practices for Biospecimen Resources, both of which were developed to address challenges around standardization of the collection and dissemination of quality biospecimens. caHUB will develop the infrastructure for collaborative biospecimen research and the production of evidence-based biospecimen standard operating procedures. | biospecimen, clinical, biomaterial supply resource, tissue |
is listed by: NIDDK Information Network (dkNET) is related to: Biorepositories and Biospecimens Research Branch has parent organization: National Cancer Institute |
Cancer | NCI ; ARRA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156094 | SCR_009657 | The Cancer Human Biobank, cancer Human Biobank | 2026-07-28 09:42:28 | 0 | |||||
|
SPRING Resource Report Resource Website 10+ mentions |
SPRING (RRID:SCR_023578) | software resource, data access protocol, web service | Interactive web tool to visualize single cell data using force directed graph layouts. Kinetic interface for visualizing high dimensional single cell expression data. Collection of pre-processing scripts and web browser based tool for visualizing and interacting with high dimensional data. | visualizing high dimensional single cell expression data, single cell expression data visualization, high dimensional data, | has parent organization: Harvard University; Cambridge; United States | NIGMS 5T32GM080177; NCI 1R33CA212697; Burroughs-Wellcome Career Award at the Scientific Interface ; Edward J Mallinckrodt Foundation Fellowship |
PMID:29228172 | Free, Available for download, Freely available | https://github.com/AllonKleinLab/SPRING/, https://github.com/AllonKleinLab/SPRING_dev | SCR_023578 | 2026-07-28 09:45:57 | 24 | |||||||
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HemOnc Knowledgebase Resource Report Resource Website 1+ mentions |
HemOnc Knowledgebase (RRID:SCR_023436) | disease-related portal, data or information resource, topical portal, portal | Medical wiki of interventions, regimens, and general information relevant to fields of hematology and oncology. Knowledge base for hematology and oncology providers, containing details about hematology/oncology drugs and treatment regimens. Any healthcare professional can sign up to contribute. Acuracy and completeness of content is overseen by Editorial Board. | Hematology and oncology knowledge base, hematology providers, oncology providers, hematology reference, oncology reference, hematology, oncology, drug interventions, treatment regimens, reference, healthcare professional, | cancer | NCI U24 CA265879 | Free, Freely available | https://hemonc.org/wiki/ | SCR_023436 | , HemOnc, Free Hematology/Oncology Reference, HemOnc.org | 2026-07-28 09:45:55 | 4 | |||||||
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Hetnet Connectivity Search Resource Report Resource Website 1+ mentions |
Hetnet Connectivity Search (RRID:SCR_023630) | Hetnet | software resource, data access protocol, web service | Web app that allows users to search for the most important paths connecting any two nodes in Hetionet. | Hetionet, paths connection, paths search, paths connecting any two nodes in Hetionet, | Pfizer Inc ; NHGRI T32 HG000046; NHGRI R01 HG010067; NCI R01 CA237170; Gordon and Betty Moore Foundation |
PMID:36711546 | Free, Freely available | SCR_023630 | , Heterogeneous network Connectivity Search, heterogeneous network | 2026-07-28 09:45:59 | 1 | |||||||
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Kinase Enrichment Analysis 3 Resource Report Resource Website 10+ mentions |
Kinase Enrichment Analysis 3 (RRID:SCR_023623) | KEA3 | software resource, data access protocol, web service | Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations. | overrepresentation of upstream kinases, upstream kinases, upstream kinases substrates, user inputted list of proteins, | has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA | NHLBI U54 HL127624; NCI U24 CA224260; NIGMS T32 GM062754; NIH Office of the Director OT3 OD025467 |
PMID:34019655 | Free, Freely available | SCR_023623 | 2026-07-28 09:45:58 | 11 | |||||||
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GeneRanger Resource Report Resource Website |
GeneRanger (RRID:SCR_023622) | software resource, data access protocol, web service | Web server application that provides access to processed data about expression of human genes and proteins across human cell types, tissues, and cell lines from several atlases. Used to explore single gene expression across tissues and cell types. | explore single gene expression, gene expression across tissues and cell types, gene expression, |
is related to: TargetRanger has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U24CA264250; NCI U24CA224260; NIDDK R01DK131525; NIH Office of the Director OT2OD030160; NIDDK RC2DK131995; NCI U24CA271114 |
PMID:37166966 | Free, Freely available | SCR_023622 | 2026-07-28 09:45:56 | 0 | ||||||||
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TargetRanger Resource Report Resource Website 1+ mentions |
TargetRanger (RRID:SCR_023621) | software resource, data access protocol, web service | Web server application that identifies targets from user inputted RNA-seq samples collected from cells we wish to target. By comparing inputted samples with processed RNA-seq and proteomics data from several atlases, TargetRanger identifies genes that are highly expressed in target cells while lowly expressed across normal human cell types, tissues, and cell lines. | identify targets, identify genes, user inputted RNA-seq samples, target cells, proteomics data, human cells, |
is related to: GeneRanger has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U24CA264250; NCI U24CA224260; NIDDK R01DK131525; NIH Office of the Director OT2OD030160; NIDDK RC2DK131995; NCI U24CA271114 |
PMID:37166966 | Free, Freely available | https://maayanlab.github.io/Workshop.io/generanger | SCR_023621 | 2026-07-28 09:45:59 | 2 | |||||||
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NCI Site Recode ICD-O-3/WHO 2008 Definition Resource Report Resource Website 1+ mentions |
NCI Site Recode ICD-O-3/WHO 2008 Definition (RRID:SCR_024687) | disease-related portal, data or information resource, topical portal, portal | Website describing International Classification of Diseases-Oncology codes that corresponds to different cancer sites in the Surveillance, Epidemiology, and End Results (SEER) registry. | NIH, International Classification of Diseases-Oncology codes, different cancer sites, Surveillance, Epidemiology, and End Results registry, SEER registry, | cancer | NCI | Free, Freely available | SCR_024687 | , National Cancer Institute Site Recode ICD-O-3/WHO 2008 Definition | 2026-07-28 09:46:09 | 3 | ||||||||
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Cancer Biomedical Informatics Grid Resource Report Resource Website 10+ mentions |
Cancer Biomedical Informatics Grid (RRID:SCR_003328) | data or information resource, organization portal, knowledge environment, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. It has been integrated into the National Cancer Informatics Program (NCIP). The National Cancer Institute launched the cancer Biomedical Informatics Grid (caBIG) to create a virtual network of interconnected data, individuals, and organizations that worked together to redefine how cancer research is conducted. caBIG capabilities allowed researchers and clinicians to collaborate more effectively so that complex research questions might be asked and answered faster and more effectively. The mission of caBIG was to develop a truly collaborative information network that accelerated the discovery of new approaches for the detection, diagnosis, treatment, and prevention of cancer, ultimately improving patient outcomes. | data sharing |
is related to: caTIES - Cancer Text Information Extraction System is related to: caArray has parent organization: National Cancer Institute is parent organization of: caTRIP |
NCI | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31949 | SCR_003328 | caBIG | 2026-07-28 09:40:41 | 32 | |||||||
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Transdisciplinary Tobacco Use Research Centers Resource Report Resource Website |
Transdisciplinary Tobacco Use Research Centers (RRID:SCR_006858) | TTURC | disease-related portal, data or information resource, topical portal, portal | A transdisciplinary approach to the full spectrum of basic and applied research on tobacco use to reduce the disease burden of tobacco use, including: * Etiology of tobacco use and addiction * Impact of advertising and marketing * Prevention of tobacco use * Treatment of tobacco use and addiction * Identification of biomarkers of tobacco exposure * Identification of genes related to addiction and susceptibility to harm from tobacco Goals * Increase the number of investigators from relevant disciplines who focus on the study of tobacco use as part of transdisciplinary teams. * Generate basic research evidence to improve understanding of the etiology and natural history of tobacco use. * Produce evidence-based tobacco use interventions that can translate to the community and specific understudied or underserved populations. * Increase the number of evidence-based interventions that are novel, including the development, testing and dissemination of innovative behavioral treatments and prevention strategies based upon findings from basic research. * Train transdisciplinary investigators capable of conducting cutting-edge tobacco use research. * Increase the number of peer-reviewed publications in the areas of tobacco use, nicotine addiction, and treatment. | gene, genetic factor, addiction gene, behavioral treatment, biomarker, molecule, nicotine use disorder, prevention, psychosocial factor, smoking, smoking cessation, tobacco exposure, treatment, nicotine, prevention, tobacco, intervention | has parent organization: National Cancer Institute | Nicotine use disorder, Addiction | NCI ; NIDA ; NIAAA |
nif-0000-24133 | SCR_006858 | 2026-07-28 09:41:44 | 0 | |||||||
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NCI Office of Biospecimens Resource Report Resource Website 1+ mentions |
NCI Office of Biospecimens (RRID:SCR_007076) | OBBR | narrative resource, data or information resource, standard specification, topical portal, portal | The NCI Office of Biorepositories and Biospecimen Research (OBBR) was established in 2005 in recognition of the critical role that biospecimens play in cancer research. The OBBR is responsible for developing a common biorepository infrastructure that promotes resource sharing and team science, in order to facilitate multi-institutional, high throughput genomic and proteomic studies. OBBR is focused on the following objectives: * Establish biobanking as a new area of research, in order to determine the impact of various collection and processing protocols on the usefulness of biospecimens in genomic and proteomic studies * Disseminate first-generation Best Practices in order to harmonize policies and procedures of NCI-supported biorepositories * Develop future generations of biorepository best practices, based on the data generated in the biobanking research programs above * Promote professional oversight of biospecimen standards development by standards organizations * Develop new technologies for biorepository operations * Develop a biorepository accreditation program * Coordinate with the international biobanking community to harmonize policies and procedures to facilitate multi-national research | has parent organization: National Cancer Institute | NCI | nlx_29021 | SCR_007076 | Office of Biorepositories and Biospecimen Research, NCI OBBR, NCI Office of Biorepositories and Biospecimen Research, National Cancer Institute Office of Biorepositories and Biospecimen Research | 2026-07-28 09:41:50 | 2 | ||||||||
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ModelDB Resource Report Resource Website 100+ mentions |
ModelDB (RRID:SCR_007271) | ModelDB | service resource, data or information resource, data repository, database, storage service resource | Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions. | repository, collection, network, neuron, computational, neuroscience, model, simulation, neural, data |
is used by: NIF Data Federation lists: ModelRun is listed by: 3DVC is listed by: Biositemaps is listed by: Integrated Models is related to: SimToolDB is related to: NeuronDB is related to: NeuronVisio is related to: Integrated Manually Extracted Annotation is related to: Allen Institute for Brain Science has parent organization: Yale University; Connecticut; USA works with: MicrocircuitDB |
NIMH ; NINDS ; NCI ; Human Brain Project ; NIDCD P01 DC004732; NIDCD R01 DC009977 |
PMID:15218350 PMID:15055399 PMID:8930855 |
Free, Freely available, Acknowledgement requested | nif-0000-00004, r3d100011330 | https://doi.org/10.17616/R3P61F | SCR_007271 | Model_DB, Model Database, Model DB, Model-DB | 2026-07-28 09:41:46 | 304 | ||||
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PrediXcan Resource Report Resource Website 10+ mentions |
PrediXcan (RRID:SCR_016739) | software application, software resource, data analysis software, data processing software | Software tool to detect known and novel genes associated with disease traits and provide insights into the mechanism of these associations. Used to test the molecular mechanisms through which genetic variation affects phenotype. | detect, gene, disease, associate, trait, mechanism, molecular, variation, phenotype | NCI K12 CA139160; NCI F32CA165823; NIMH T32 MH020065; NIMH R01 MH101820; NIMH R01 MH090937; NIGMS U01 GM61393; NIMH P50 MH094267; NIGMS U01 GM092691; NHLBI U19 HL065962; NIDA P50 DA037844; NIDDK P30 DK20595; NIDDK P60 DK20595 |
PMID:26258848 | Free, Available for download, Freely available | SCR_016739 | 2026-07-28 09:44:22 | 23 | |||||||||
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ConsensusClusterPlus Resource Report Resource Website 100+ mentions |
ConsensusClusterPlus (RRID:SCR_016954) | software application, software resource, data analysis software, data processing software | Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots. | cluster, count, stability, evidence, unsupervised, analysis, , bio.tools |
is listed by: Bioconductor is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
NCI F32CA142039; Thomas G. Labrecque Foundation ; NCI U24 CA126554 |
PMID:20427518 | Free, Available for download, Freely available | biotools:consensusclusterplus | https://bio.tools/consensusclusterplus | SCR_016954 | 2026-07-28 09:44:26 | 160 | ||||||
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dcmqi Resource Report Resource Website 1+ mentions |
dcmqi (RRID:SCR_016933) | dcmqi | software application, software resource, data processing software, software library, image processing software, software toolkit | Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer. | DICOM, converter, medical, image, computing, quantitative, analysis, clinical, data, metadata, radiology, standard, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Harvard University; Cambridge; United States |
NCI U24 CA180918; NIBIB P41 EB015902; NIBIB P41 EB01589; NIBIB R01 EB014955 |
PMID:29092948 | Free, Available for download, Freely available, Tutorial available | biotools:dcmqi | https://github.com/QIICR/dcmqi, https://bio.tools/dcmqi | SCR_016933 | DICOM for Quantitative Imaging, The Digital imaging and Communications in Medicine for Quantitative Imaging, Digital imaging and Communications in Medicine for Quantitative Imaging, DCMQI | 2026-07-28 09:44:25 | 3 | ||||
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MARRVEL Resource Report Resource Website 10+ mentions |
MARRVEL (RRID:SCR_016871) | MARRVEL | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research. | integration, database, model, genetic, resource, functional, annotation, genome, data, analysis, dataset, rare, variant, exploration, bio.tools |
uses: OMIM uses: ClinVar uses: DECIPHER uses: Geno2MP uses: Database of Genomic Variants is used by: Hypothesis Center is listed by: bio.tools is listed by: Debian |
NINDS 1U54NS093793; NIH Office of the Director R24 OD022005; The Robert and Janice McNair Foundation ; Baylor College of Medicine Medical Scientist Training Program ; NINDS U54 NS093793; NIGMS R01 GM067858; NIGMS R01 GM120033; NSF DMS 1263932; CPRIT RP170387; Houston Endowment ; Huffington Foundation ; Belfer Foundation ; T T Chao Family Foundation ; NIGMS R01 GM067761; NIGMS R01 GM084947; NCRR R24 RR032668; NIH Office of the Director R24 OD021997; NCI P30 CA06516; NHGRI U01 HG007709; Simons Foundation |
PMID:28502612 | Free, Public, Freely available | biotools:marrvel | https://bio.tools/marrvel | SCR_016871 | Model organism Aggregated Resources for Rare Variant ExpLoration | 2026-07-28 09:44:25 | 22 | ||||
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Sashimiplot Resource Report Resource Website |
Sashimiplot (RRID:SCR_016861) | sashimiplot | data visualization software, software resource, software application, data processing software | Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions. | quantitative, visualization, aligned, RNA-Seq, read, data, compare, exon, usage, sample, experiment, condition, MISO | is related to: MISO | NCI R01 CA157304; Starr Cancer Consortium ; NIGMS R01 GM096193; NSF IIS 1149662; Alfred P. Sloan research fellowship ; NIGMS R01 GM085319; NCI U01 CA184897; NHGRI R01 HG002439 |
PMID:25617416 DOI:10.1093/bioinformatics/btv034 |
Free, Available for download, Freely available | http://miso.readthedocs.org/en/fastmiso/sashimi.html | SCR_016861 | sashimi_plot | 2026-07-28 09:44:25 | 0 | |||||
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Salmon Resource Report Resource Website 100+ mentions |
Salmon (RRID:SCR_017036) | software application, software resource, data analysis software, data processing software | Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias. | quantifying, expression, transcript, RNAseq, data, correct, fragment, GC, content, bias |
is listed by: Debian is listed by: OMICtools has parent organization: Stony Brook University; New York; USA has parent organization: Carnegie Mellon University; Pennsylvania; USA has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA has parent organization: Harvard University; Cambridge; Massachusetts |
Gordon and Betty Moore Foundation Data-Driven Discovery Initiative ; NHGRI R21 HG006913; NHGRI R01 HG007104; Alfred P. Sloan Research ; NCI T32 CA009337; NHGRI R01 HG005220; NSF BIO-1564917; NSF CCF-1256087; NSF CCF-1053918; NSF EF-0849899 |
PMID:28263959 | Free, Available for download, Freely available | OMICS_09075 | https://github.com/COMBINE-lab/salmon, https://sources.debian.org/src/salmon/ | SCR_017036 | 2026-07-28 09:44:28 | 357 |
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