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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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omniBiomarker Resource Report Resource Website 1+ mentions |
omniBiomarker (RRID:SCR_005750) | omniBiomarker | data analysis service, production service resource, service resource, analysis service resource | omniBiomarker is a web-application for analysis of high-throughput -omic data. Its primary function is to identify differentially expressed biomarkers that may be used for diagnostic or prognostic clinical prediction. Currently, omniBiomarker allows users to analyze their data with many different ranking methods simultaneously using a high-performance compute cluster. The next release of omniBiomarker will automatically select the most biologically relevant ranking method based on user input regarding prior knowledge. The omniBiomarker workflow * Data: Gene Expression * Algorithms: Knowledge-Driven Gene Ranking * Differentially expressed Genes * Clinical / Biological Validation * Knowledge: NCI Thesaurus of Cancer, Cancer Gene Index * back to Algorithms | gene, gene expression, algorithm, cancer, cancer gene, cancer gene index, biocomputing, biomarker, clinical, gene ranking |
has parent organization: Georgia Institute of Technology; Georgia; USA has parent organization: Emory University; Georgia; USA |
Cancer | Georgia Cancer Coalition ; NCI U54CA119338; NCI R01CA108468 |
PMID:19695674 | nlx_149210 | SCR_005750 | omniBiomarker: Knowledge-Driven Biomarker Identification and Data Combination | 2026-02-13 10:55:41 | 3 | |||||
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Cooperative Human Tissue Network Western Division at Vanderbilt University Medical Center Resource Report Resource Website |
Cooperative Human Tissue Network Western Division at Vanderbilt University Medical Center (RRID:SCR_006661) | CHTN Western Division | biomaterial supply resource, tissue bank, material resource | The Cooperative Human Tissue Network- Western Division at Vanderbilt University Medical Center is one of six institutions throughout the country funded by the National Cancer Institutes to procure and distribute remnant human tissues to biomedical researchers throughout the United States and Canada. CHTN operates through a shared networking system which allows investigators greater access to available research specimens. CHTN offers a variety of preparation and preservation techniques to ensure investigators are receiving the quality specimens needed for research. Remnant tissues are obtained from surgical resections and autopsies and are procured to the specifications of the investigator. | tissue |
lists: Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB) is listed by: One Mind Biospecimen Bank Listing is related to: Vanderbilt University Medical Center; Tennessee; USA has parent organization: Vanderbilt University; Tennessee; USA |
All | NCI | Public | nlx_143710 | SCR_006661 | CHTN Western Division at VUMC, Cooperative Human Tissue Network - Western Division, VUMC Tissue Repository | 2026-02-13 10:55:53 | 0 | |||||
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HetMatPy Resource Report Resource Website 1+ mentions |
HetMatPy (RRID:SCR_023409) | network analysis software, data processing software, data analysis software, software application, software resource | Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes. | Hetionet, matrix storage, operations on hetnets, hetnets, heterogeneous networks, | Gordon and Betty Moore Foundation ; NHGRI R01 HG010067; NCI R01 CA237170 |
PMID:36711546 | Free, Available for download, Freely available | SCR_023409 | hetmatpy | 2026-02-13 10:58:59 | 1 | ||||||||
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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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CancerModels.Org Resource Report Resource Website 1+ mentions |
CancerModels.Org (RRID:SCR_023931) | data repository, storage service resource, portal, data or information resource, service resource, disease-related portal, topical portal | Cancer research platform that aggregates clinical, genomic and functional data from various types of patient derived cancer models, xenographs, organoids and cell lines. Open catalog of harmonised patient-derived cancer models. Standardises, harmonises and integrates clinical metadata, molecular and treatment-based data from academic and commercial providers worldwide. Data is FAIR and underpins generation and testing of new hypotheses in cancer mechanisms and personalised medicine development. PDCM Finder have expanded to organoids and cell lines and is now called CancerModels.Org. PDCM Finder was launched in April 2022 as successor of PDX Finder portal, which focused solely on patient-derived xenograft models. | FAIR data, clinical data, genomic data, functional data, patient derived, cancer models, xenographs, organoids, cell lines, | cancer | NCI U24 CA204781 01; NCI U24 CA253539 01; NCI R01 CA089713 |
PMID:36399494 | Free, Freely available | r3d100012961 | https://doi.org/10.17616/R31NJMHT | SCR_023931 | PDCM Finder, PDX Finder | 2026-02-13 10:59:04 | 7 | |||||
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RiboToolkit Resource Report Resource Website 1+ mentions |
RiboToolkit (RRID:SCR_024406) | data access protocol, software resource, web service | Integrated web server developed for Ribo-seq data analysis. Platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.Web based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs. | Ribo-seq data analysis, analysis and annotation of ribosome profiling data, decode mRNA translation at codon resolution, data cleaning and quality evaluation, | NCI R35 CA232115 | PMID:32427338 | Free, Freely available | SCR_024406 | 2026-02-13 10:59:13 | 2 | |||||||||
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NCI SEER Cancer Statistics Review Resource Report Resource Website 100+ mentions |
NCI SEER Cancer Statistics Review (RRID:SCR_024685) | portal, data or information resource, disease-related portal, topical portal | Platform to report outlining trends in cancer statistics and methods to derive various cancer statistics from the Surveillance, Epidemiology, and End Results (SEER) program. Authoritative source for cancer statistics in the United States. | trends in cancer, cancer statistics, methods to derive various cancer statistics, Surveillance, Epidemiology, and End Results program, SEER program, | cancer | NCI | Free, Freely available | https://seer.cancer.gov/ | SCR_024685 | SEER Cancer Statistics Review, , National Cancer Institute SEER Cancer Statistics Review, NIH NCI Surveillance, Epidemiology, and End Results Cancer Statistics Review, NIH NCI SEER Cancer Statistics Review | 2026-02-13 10:59:17 | 345 | |||||||
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NCI Lymphoid Neoplasm Recode 2020 Revision Definition Resource Report Resource Website |
NCI Lymphoid Neoplasm Recode 2020 Revision Definition (RRID:SCR_024686) | portal, data or information resource, disease-related portal, topical portal | Website describing International Classification of Diseases codes that corresponds to lymphomas in the Surveillance, Epidemiology, and End Results (SEER) registry. | International Classification of Diseases codes, ICD, lymphoma, Surveillance, Epidemiology, and End Results registry, SEER registry, | lymphomas | NCI | Free, Available for download, Freely available | https://seer.cancer.gov/lymphomarecode/lymphoma-2021.html | SCR_024686 | , Lymphoid Neoplasm Recode 2020 Revision Definition, National Cancer Institute Lymphoid Neoplasm Recode 2020 Revision Definition, NIH NCI Lymphoid Neoplasm Recode 2020 Revision Definition | 2026-02-13 10:59:15 | 0 | |||||||
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OpenMM Resource Report Resource Website 10+ mentions |
OpenMM (RRID:SCR_000436) | software resource, simulation software, standalone software, software application | Software toolkit to run modern molecular simulations. It can be used either as a standalone application for running simulations, or as a library that enables accelerated calculations for molecular dynamics on high-performance computer architectures. | modeling, molecular dynamics, molecular simulation |
is used by: CHARMM-GUI is listed by: Simtk.org has parent organization: Stanford University; Stanford; California |
NIGMS U54 GM072970; NIGMS R01 GM062868; NCI P30 CA008748 |
PMID:28746339 PMID:23316124 PMID:38154096 DOI:10.1021/acs.jpcb.3c06662 |
Free, Available for download, Freely available | nif-0000-23334 | https://github.com/openmm/openmm https://openmm.org/ https://openmm.org/documentation https://github.com/openmm |
https://simtk.org/home/openmm | SCR_000436 | OpenMM 8, OpenMM, OpenMM 7, OpenMM 4 | 2026-02-13 10:54:40 | 12 | ||||
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DCTD Resource Report Resource Website 10+ mentions |
DCTD (RRID:SCR_004196) | DCTD | data or information resource, funding resource, portal | Division of NCI that takes prospective cancer detection and treatment leads, facilitates their paths to clinical application, and expedites the initial and subsequent large-scale testing of new agents, biomarkers, imaging tests, and other therapeutic interventions (radiation, surgery, immunotherapy) in patients. DCTD, like all of NCI, supports many programs that could not be done without government funding - investigators supported by the division engage in scientifically sound, high-risk research that may yield great benefits for patients with cancer, but are too difficult or risky for industry or academia to pursue. This includes a particular emphasis on the development of distinct molecular signatures for cancer, refined molecular assays, and state-of-the-art imaging techniques that will guide oncologic therapy in the future. The division has eight major programs that work together to bring unique molecules, diagnostic tests, and therapeutic interventions from the laboratory bench to the patient bedside: * Cancer Diagnosis Program * Cancer Imaging Program * Cancer Therapy Evaluation Program * Developmental Therapeutics Program * Radiation Research Program * Translational Research Program * Biometrics Research Branch * Office of Cancer Complementary and Alternative Medicine | treatment, diagnosis, molecule, diagnostic test, therapeutic intervention |
is listed by: OMICtools has parent organization: National Cancer Institute is parent organization of: CDP |
Cancer | NCI | OMICS_01537 | SCR_004196 | Division of Cancer Treatment and Diagnosis | 2026-02-13 10:55:23 | 18 | ||||||
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GoMiner Resource Report Resource Website 100+ mentions |
GoMiner (RRID:SCR_002360) | GoMiner | software resource, data processing software, software application | GoMiner is a tool for biological interpretation of "omic" data including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samples, raising the question, What does it all mean biologically? To answer this question, GoMiner leverages the Gene Ontology (GO) to identify the biological processes, functions and components represented in these lists. Instead of analyzing microarray results with a gene-by-gene approach, GoMiner classifies the genes into biologically coherent categories and assesses these categories. The insights gained through GoMiner can generate hypotheses to guide additional research. GoMiner displays the genes within the framework of the Gene Ontology hierarchy in two ways: * In the form of a tree, similar to that in AmiGO * In the form of a "Directed Acyclic Graph" (DAG) The program also provides: * Quantitative and statistical analysis * Seamless integration with important public databases GoMiner uses the databases provided by the GO Consortium. These databases combine information from a number of different consortium participants, include information from many different organisms and data sources, and are referenced using a variety of different gene product identification approaches. | experiment, expression, function, gene, genomics, biological, genomic, microarray, omic, process, gene expression, gene ontology, biological process, biological function, biological component, proteomic, database, FASEB list |
is related to: Gene Ontology is related to: High-Throughput GoMiner has parent organization: Georgia Institute of Technology; Georgia; USA has parent organization: Emory University; Georgia; USA has parent organization: National Cancer Institute |
NCI ; Georgia Institute of Technology; Georgia; USA ; Emory University; Georgia; USA |
PMID:12702209 | nif-0000-21181 | SCR_002360 | 2026-02-13 10:55:01 | 115 | |||||||
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DeepNeuro Resource Report Resource Website 1+ mentions |
DeepNeuro (RRID:SCR_016911) | software resource, software toolkit | Software Python package for neuroimaging data. Framework to design and train neural network architectures. Used in medical imaging community to ensure consistent performance of networks across variable users, institutions, and scanners. | Design and train neural network architectures, medical imaging, neuroimaging data, neuroimaging |
uses: Python Programming Language is related to: Massachusetts General Hospital has parent organization: Harvard University; Cambridge; United States |
NIDA T90 DA022759; NIDA R90 DA023427; NIH Blueprint for Neuroscience Research ; NIBI ; NIBIB T32 EB1680; NCI U01 CA154601; NCI U24 CA180927; NCI U24 CA180918; NIBIB P41 EB015896 |
PMID:32578020 | Free, Available for download, Freely available | SCR_016911 | 2026-02-13 10:57:48 | 2 | ||||||||
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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 | 2026-02-13 10:58:28 | 2 | ||||||||
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xHLA Resource Report Resource Website 1+ mentions |
xHLA (RRID:SCR_022277) | software resource, data processing software, software application | Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer. | HLA typing, short read sequence data, refines mapping results, amino acid level, four digit typing accuracy | NCI 5U24CA076518; NHLBI 5U10HL069294; Health Resources and Services Administration ; Office of Naval Research Grants |
PMID:28674023 | Free, Available for download, Freely available | SCR_022277 | 2026-02-13 10:58:46 | 2 | |||||||||
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arcasHLA Resource Report Resource Website 1+ mentions |
arcasHLA (RRID:SCR_022286) | software resource, data processing software, software application | Software tool for high resolution HLA typing from RNAseq. Fast and accurate in silico inference of HLA genotypes from RNA-seq. | in silico inference of HLA genotypes, RNA-seq data, HLA typing | DARPA ; Phillip A. Sharp award ; NCI U54CA193313; NIGMS R01GM117591 |
PMID:31173059 | Free | SCR_022286 | 2026-02-13 10:58:40 | 8 | |||||||||
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Harvard Medical School Center for Cancer Systems Pharmacology Resource Report Resource Website |
Harvard Medical School Center for Cancer Systems Pharmacology (RRID:SCR_022831) | CCSP | data or information resource, organization portal, portal | Center includes studies for responsiveness and resistance to anti cancer drugs. Committed to training students and postdocs, promoting junior faculty and ensuring that data and software are reproducible, reliable and publicly accessible. Member of National Cancer Institute’s Cancer Systems Biology Consortium. | anti cancer drugs, responsiveness and resistance, National Cancer Institute, Systems Biology Consortium. | has parent organization: Harvard University; Cambridge; United States | Cancer, Melanoma, Triple negative breast cancer (TNBC), Glioblastoma multiforme (GBM) | NCI U54 CA225088 | Free, Freely available | SCR_022831 | Center for Cancer Systems Pharmacology | 2026-02-13 10:58:48 | 0 | ||||||
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Ohio State Leukemia Tissue Bank Resource Report Resource Website |
Ohio State Leukemia Tissue Bank (RRID:SCR_000529) | LTBSR | biomaterial supply resource, tissue bank, material resource | The OSU Comprehensive Cancer Center Leukemia Tissue Bank Shared Resource (LTBSR) facilitates the successful translation of basic leukemia research to the clinical setting via an extensive repository of tissue samples and accompanying pathologic, cytogenetic and clinical data for ready correlation of clinical and biological results. The LTBSR, which is an NCI-sponsored biorepository, has more than 40,000 vials of cryopreserved viable cells and 13,000 vials of matched frozen plasma and/or serum samples from more than 4,000 patients treated for leukemia and other malignancies. Committed to furthering translational research efforts for OSUCCC - James members and the cancer research community, the LTBSR provides investigators with training and technical support as well as procurement, processing, storage, retrieval and distribution of clinical research materials. In many cases, the LTBSR serves as the central processing lab for multi-site trials in which the principal investigator is an OSUCCC - James member. The LTBSR's goals are to: * Provide a central collection, processing and a state-of-the-art repository for samples collected from leukemia patients treated on OSUCCC - James protocols, and * Provide materials to investigators involved in collaborative studies with OSU, who examine relevant cellular and molecular properties of leukemia and correlate these properties with clinical or population-based outcomes. | leukemia, tissue, plasma, serum, cell, cells, viable cells, cryopreserved viable cells, pathologic data, cytogenetic data, clinical data, frozen, cryopreserved, malignancy, cancer |
is listed by: One Mind Biospecimen Bank Listing has parent organization: OSUCCC-James |
Leukemia, Cancer | NCI 2P30CA016058-40 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_55663 | http://www.osuccc.osu.edu/11167.cfm | SCR_000529 | OSUCCC Leukemia Tissue Bank Shared Resource, OSUCCC LTBSR, OSU Comprehensive Cancer Center Leukemia Tissue Bank Shared Resource | 2026-02-13 10:54:41 | 0 | ||||
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CPCTR: Cooperative Prostate Cancer Tissue Resource Resource Report Resource Website 1+ mentions |
CPCTR: Cooperative Prostate Cancer Tissue Resource (RRID:SCR_000803) | CPCTR | biomaterial supply resource, tissue bank, material resource | THIS RESOURCE IS NO LONGER IN SERVICE. Doumented on September 23,2022. The National Cancer Institute initially established the Cooperative Prostate Cancer Tissue Resource (CPCTR) to provide prostate cancer tissue samples with clinical annotation to researchers. The Resource provides access to formalin-fixed, paraffin-embedded primary prostate cancer tissue with associated clinical and follow-up data for research studies, particularly studies focused on translating basic research findings into clinical application. Fresh-frozen tissue is also available with limited clinical follow up information since these are more recent cases. The Resource database contains pathologic and clinical information linked to a large collection of prostate tissue specimens that is available for research. Researchers can determine whether the Resource has the tissues and patient data they need for their individual research studies. Consultation and interpretive services: Assistance is available from trained CPCTR pathologists. The CPCTR can provide consultative assistance in staining interpretation, and scoring, on a collaborative basis. Fresh Frozen and Paraffin Tissue: The resource has over 7,000 annotated cases (including 7,635 specimens and 38,399 annotated blocks). Tissue Microarrays (TMA): The CPCTR has slides from prostate cancer TMAs with associated clinical data. The information provided for each case on the arrays (derived from radical prostatectomy specimens) includes: age at diagnosis, race, PSA at diagnosis, tumor size, TNM stage, Gleason score and grade, and vital status and other variables. | prostate cancer, tissue microarray, fresh frozen, paraffin tissue, tumor, tissue, primary prostate cancer tissue, clinical data, follow-up data, outcome data, formalin-fixed paraffin-embedded |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Pittsburgh; Pennsylvania; USA |
Prostate cancer | NCI CA086772 | PMID:15269132 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143725 | SCR_000803 | Cooperative Prostate Cancer Tissue Resource | 2026-02-13 10:54:44 | 2 | ||||
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Human Reference Protein Interactome Project Resource Report Resource Website 10+ mentions |
Human Reference Protein Interactome Project (RRID:SCR_015670) | HuRI | web application, portal, data or information resource, software resource, database, project portal | Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies. | protein interactome, protein-protein interaction, ppi, pairwise combination, proteome, human reference | NHGRI R01/U01HG001715; NHGRI P50HG004233; NHLBI U01HL098166; NHLBI U01HL108630; NCI U54CA112962; NCI R33CA132073; NIH RC4HG006066; NICHD ARRA R01HD065288; NICHD ARRA R21MH104766; NICHD ARRA R01MH105524; NIMH R01MH091350; NSF CCF-1219007; NSERC RGPIN-2014-03892 |
PMID:25416956 | Freely Available, Free, Available for download | SCR_015670 | HuRI: The Human Reference Protein Interactome Mapping Project | 2026-02-13 10:57:39 | 20 | |||||||
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tximport Resource Report Resource Website 50+ mentions |
tximport (RRID:SCR_016752) | data analysis software, software resource, data processing software, software application | Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. | pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools works with: edgeR works with: DESeq2 |
SNSF 143883; European Commission ; NCI T32 CA009337 |
DOI:10.12688/f1000research.7563.1 | Free, Available for download, Freely available | biotools:tximport | https://bioconductor.org/packages/tximport/ https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html https://github.com/F1000Research/tximport https://bio.tools/tximport |
https://zenodo.org/record/35123#.W_w3behKiM8 | SCR_016752 | tximport v1.4.0 | 2026-02-13 10:57:50 | 91 |
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