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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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AACR GENIE cBioPortal Resource Report Resource Website 10+ mentions |
AACR GENIE cBioPortal (RRID:SCR_026217) | consortium, organization portal, data or information resource, portal | International data-sharing consortium focused on generating an evidence base for precision cancer medicine by integrating clinical-grade cancer genomic data with clinical outcome data of cancer patients treated at multiple institutions worldwide. | International data-sharing consortium, generating an evidence base, precision cancer medicine, integrating clinical-grade cancer genomic data, clinical outcome data, cancer patients, | NCI CA008748; Howard Hughes Medical Institute ; NCI 5U01CA168394; NCI 5P50CA098258; NCI 5P50CA083639; NHGRI U54HG008100; NCI U24CA210950; NCI U24CA209851; NCI 2P30CA006516; NCI 5P30CA068485; NCI CA006973; NCI CA121113; NCI CA180950 |
PMID:28572459 | Restricted | SCR_026217 | 2026-08-03 09:38:44 | 13 | |||||||||
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Strainy Resource Report Resource Website |
Strainy (RRID:SCR_026430) | software resource, software application, source code | Software tool for phasing and assembly of bacterial strains from long-read sequencing data (either Oxford Nanopore or PacBio). Given reference (or collapsed de novo assembly) and set of aligned reads as input, tool produces multi-allelic phasing, individual strain haplotypes and strain-specific variant calls. Used for phasing and assembly of strain haplotypes from long-read metagenome sequencing. | phasing and assembly, strain haplotypes, long-read metagenome sequencing, | NCI | PMID:39327484 | Free, Available for download, Freely available | SCR_026430 | 2026-08-03 09:38:48 | 0 | |||||||||
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xCell Resource Report Resource Website 50+ mentions |
xCell (RRID:SCR_026446) | software toolkit, software resource, source code, web application | Software R package for generating cell type scores and R scripts for development of xCell. Web tool that performs cell type enrichment analysis from gene expression data for immune and stroma cell types. Used for Cell types enrichment analysis. | Cell types enrichment analysis, cell type, enrichment analysis, generating cell type scores and R scripts, development of xCell, | Gruss Lipper Postdoctoral Fellowship ; NCI U24 CA195858; NIAID |
PMID:29141660 | Free, Available for download, Freely available | http://xCell.ucsf.edu/ | SCR_026446 | 2026-08-03 09:39:17 | 62 | ||||||||
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NetworkDataCompanion Resource Report Resource Website 1+ mentions |
NetworkDataCompanion (RRID:SCR_026532) | software library, software toolkit, software resource, source code | Software R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo. Streamlines routine steps in TCGA data processing, including filtering and mapping gene and sample identifiers between modalities and allows modality-specific data transformation, such as normalization and cleaning. | TCGA and GTEx data analysis, TCGA data processing, filtering and mapping gene, normalization and cleaning, | NCI R35CA220523; NCI U24CA231846; NCI P50CA127003; NHGRI R01HG011393; NHGRI R01HG125975; NHLBI P01HL114501; NHLBI T32HL007427; NHLBI K01HL166376; American Lung Association |
PMID:39574772 | Free, Available for download, Freely available | SCR_026532 | 2026-08-03 09:39:18 | 1 | |||||||||
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Borzoi Resource Report Resource Website 1+ mentions |
Borzoi (RRID:SCR_026619) | software toolkit, software resource, source code | Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences. | Borzoi models access, convolutional neural networks, predict RNA-seq coverage, | Common Fund of the Office of the Director ; NCI ; NHGRI ; NHLBI ; NIDA ; NIMH ; NINDS |
PMID:39779956 | Free, Available for download, Freely available | SCR_026619 | 2026-08-03 09:38:58 | 1 | |||||||||
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PathoMAN Resource Report Resource Website |
PathoMAN (RRID:SCR_026552) | PathoMAN | software resource, web application | Web application to automate germline genomic variant curation from clinical sequencing based on ACMG guidelines. Aggregates multiple tracks of genomic, protein and disease specific information from public sources. | Aggregates multiple tracks, automate germline genomic variant curation, clinical sequencing, genomic, protein, disease specific information, public sources, | NCI R21CA029533; NCI P50CA221745; NCI P30CA008748 |
PMID:30787465 | Free, Freely available, | SCR_026552 | Pathogenicity of Mutation Analyzer | 2026-08-03 09:38:57 | 0 | |||||||
|
PEtab Resource Report Resource Website |
PEtab (RRID:SCR_026915) | software resource, source code | Repository contains PEtab specifications and additional documentation. Data format for specifying parameter estimation problems in systems biology. SBML and TSV based data format for parameter estimation problems in systems biology. Human- and computer- readable format for representing parameter estimation problems in systems biology. | SBML, TSV, data format, parameter estimation problems, systems biology, specifying parameter estimation problems, | European Unions Horizon 2020 ; NCI U54 CA225088 |
PMID:33497393 | Free, Available for download, Freely available | https://github.com/PEtab-dev/PEtab, https://zenodo.org/records/3732958 | SCR_026915 | 2026-08-03 09:39:23 | 0 | ||||||||
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SigProfilerAssignment Resource Report Resource Website 1+ mentions |
SigProfilerAssignment (RRID:SCR_026899) | software resource, software application, source code | Software tool for assignment of known mutational signatures to individual samples and individual somatic mutations. | assignment of known mutational signatures, individual samples, individual somatic mutations, | Cancer Research UK Grand Challenge Award ; NIEHS R01ES030993; NIEHS R01ES032547; NCI R01CA269919; Packard Fellowship for Science and Engineering |
PMID:37502962 | Free, Available for download, Freely available, | SCR_026899 | 2026-08-03 09:39:02 | 3 | |||||||||
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CLEAR Resource Report Resource Website |
CLEAR (RRID:SCR_027171) | software toolkit, software resource, source code | Software workflow that identifies reliably quantifiable transcripts in limiting-cell RNA-seq (lcRNA-seq) data for differentially expressed genes (DEG) analysis. Coverage-based Limiting-cell Experiment Analysis for RNA-seq. | RNA-seq, cell experiment analysis for RNA-seq, | NCI P30 CA016058; NCI R50 CA211524; Ohio State University |
PMID:32039730 | GNU General Public License v3.0 | SCR_027171 | , CLEAR: Coverage-based Limiting-cell Experiment Analysis for RNA-seq, Coverage-based Limiting-cell Experiment Analysis for RNA-seq | 2026-08-03 09:39:03 | 0 | ||||||||
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RAIDS (Robust Ancestry Inference using Data Synthesis) Resource Report Resource Website |
RAIDS (Robust Ancestry Inference using Data Synthesis) (RRID:SCR_027265) | RAIDS | software application, data processing software, data analysis software, simulation software, software resource | Software R package to enable genetic ancestry inference from various cancer sequence sources (RNA, Exome, and Whole-Genome sequences). This package also implements simulation algorithm that generates synthetic cancer-derived data. Used for accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms | genetic ancestry, inference of genetic ancestry, cancer-derived molecular data, generate synthetic cancer-derived data, | NCI P30CA45508; NCI P20CA192996; NCI U01CA224013; NCI U01CA210240; NCI R01CA188134; NCI R01CA249002; NCI R01CA229699 |
PMID:36351074 | Free, Available for download, Freely Available | https://github.com/KrasnitzLab/RAIDS | SCR_027265 | , Robust Ancestry Inference using Data Synthesis (RAIDS), Robust Ancestry Inference using Data Synthesis | 2026-08-03 09:39:26 | 0 | ||||||
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SEAHORSE Resource Report Resource Website |
SEAHORSE (RRID:SCR_027399) | data or information resource, database | Web-based database and search tool for exploratory data analysis in which we have pre-computed statistical associations between available data elements. Large-scale, open-access data sets such as the Genotype Tissue Expression Project (GTEx) and The Cancer Genome Atlas (TCGA) include multi-omic data on large numbers of samples along with extensive clinical and phenotypic information. Allows users to explore significant associations using tabulated summary statistics, data visualizations, and functional enrichment analyses (using RNA-seq data) for identified sets of genes. | Unexpected Correlations, Large Cohort Studies, Gene Expression, Gene Regulatory Networks, Correlations | NCI R35 CA220523; NHGRI R01 HG011393; NCI U24 CA231846 |
DOI:10.1101/2025.08.15.670514v1 | Free, Freely available, | SCR_027399 | Serendipity Engine Assaying Heterogeneous Omics Related Sampling Experiments | 2026-08-03 09:39:09 | 0 | ||||||||
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BayesPrism Resource Report Resource Website 1+ mentions |
BayesPrism (RRID:SCR_027499) | software toolkit, software resource, source code | Software R package for fully Bayesian inference of tumor microenvironment composition and gene expression deconvolution. Used to analyze bulk RNA-seq data and estimate cell type-specific expression profiles. | tumor microenvironment composition, gene expression deconvolution, analyze bulk RNA-seq data, estimate cell type-specific expression profiles, | NHGRI R01 HG009309; NCI U2C CA288284; NCI U54 CA209975 |
PMID:35469013 | Free, Available for download, Freely available | SCR_027499 | 2026-08-03 09:39:11 | 8 | |||||||||
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CytoSPACE Resource Report Resource Website 1+ mentions |
CytoSPACE (RRID:SCR_027634) | software resource, software application, source code | Software tool for assigning single cells from scRNA-seq to spatial transcriptomics coordinates via optimization framework. Supports high-resolution cell/spot alignment, capacity-constrained/domain-aware placement, and outputs per-cell/per-spot assignments and probabilities for downstream visualization and analysis. Used for optimal mapping of scRNA-seq data to spatial transcriptomics data. | Optimal mapping of scRNA-seq data to spatial transcriptomics data, assigning single cells from scRNA-seq, spatial transcriptomics coordinates, optimization framework, mapping, scRNA-seq data, spatial transcriptomics data, | American Association for Cancer Research ; Norwegian Cancer Society ; NCI R01CA255450; NCI R00CA187192; NCI R21CA238971; Virginia and D. K. Ludwig Fund for Cancer Research ; Donald E. and Delia B. Baxter Foundation |
PMID:36879008 | Free, Available for download, Freely available | https://github.com/digitalcytometry/cytospace | SCR_027634 | 2026-08-03 09:39:11 | 8 | ||||||||
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METAFlux Resource Report Resource Website |
METAFlux (RRID:SCR_028022) | software resource, software application, source code | Software tool that predicts cancer metabolic fluxes from bulk RNA-seq and scRNA-seq data to address these analytic gaps. Used for characterizing metabolic circuits and output non-degenerative fluxes using cancer gene expression data. | predict cancer metabolic fluxes, RNA-seq data, scRNA-seq data, characterizing metabolic circuits, non-degenerative fluxes, cancer gene expression data, | NCI U01CA247760; NCI P30 CA016672; Chan Zuckerberg Initiative ; Silicon Valley Community Foundation ; MD Anderson Moonshot programs |
PMID:37573313 | Free, Available for download, Freely available | SCR_028022 | 2026-08-03 09:39:17 | 0 | |||||||||
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CivicDb Resource Report Resource Website |
CivicDb (RRID:SCR_028055) | knowledge base, data or information resource, database | Open-access, community-driven knowledgebase designed to crowdsource and curate evidence on the clinical significance of cancer-related genomic variants. It helps researchers and clinicians interpret tumor DNA mutations to guide precision medicine. | clinical significance of cancer-related genomic variants, cancer-related genomic variants, genomic variants, | is related to: ClinGen | NCI U01CA209936; NCI U24CA237719; NCATS UL1TR002345; NHGRI U41 HG008735; NHGRI R00HG010157; NHGRI R00HG007940; NCI K22CA188163 |
PMID:36373660 | Free, Freely available, | SCR_028055 | , Clinical Interpretation of Variants in Cancer, CIViCdb | 2026-08-03 09:39:25 | 0 | |||||||
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EpiProfile Resource Report Resource Website |
EpiProfile (RRID:SCR_028224) | software resource, software application, source code | Software tool for processing Epi-Proteomics mass spectrometry data. Discriminates isobaric histone peptides using distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry-based quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples. EpiProfile 2.0 is extended version of v1.0 for enhanced quantification of histone peptides based on LC-MS/MS analysis. | LC-MS/MS analysis, peptide, quantification, histone, quantification of histone peptides, quantification of histone peptides based on LC-MS/MS analysis, mass spectrometry data, | NIGMS GM110174; NIAID AI118891; NCI CA196539; UPenn Epigenetics Institute ; NCATS TL1TR001880; NIGMS T32GM008275 |
PMID:25805797 PMID:29790754 |
Free, Available for download, Freely available | SCR_028224 | EpiProfile 2.0 | 2026-08-03 09:39:39 | 0 | ||||||||
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HiTAIC Resource Report Resource Website |
HiTAIC (RRID:SCR_028181) | web service, data access protocol, software resource | Web-based application to trace tumor tissue of origin in primary and metastasized cancers. | Tumor classifier, trace tumor tissue of origin, primary and metastasized cancers, | NIGMS P20GM104416; NCI R01CA253976; NCI R01CA216265; NCI R01CA275974; NCI P30CA023108 |
PMID:37089814 | Free, Freely available | SCR_028181 | Hierarchical Tumor Artificial Intelligence Classifier | 2026-08-03 09:39:39 | 0 | ||||||||
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University of Miami Sylvester Cancer Proteomics Shared Resource Core Facility Resource Report Resource Website |
University of Miami Sylvester Cancer Proteomics Shared Resource Core Facility (RRID:SCR_028491) | service resource, access service resource, core facility | Core provides advanced mass spectrometry-based proteomics to support basic, translational, and clinical cancer research. Delivers high quality, quantitative proteomic data using instrumentation, including Thermo Scientific Astral Zoom and Ascend Tribrid orbitrap mass spectrometers. Services include gel band protein identification, immunoprecipitation and pulldown proteomics, cleavable cross-linking mass spectrometry, and global quantitative proteomics and post‑translational modification analysis using tandem mass tag‑based multiplexing or label‑free data-independent acquisition and data-dependent acquisition approaches. The CPSR supports end-to-end proteomics pipelines—from whole cells and primary tumor organoids through quantitative analysis and data visualization—providing comprehensive “soup to nuts” analytical capability. | ABRF, mass spectrometry, proteomics services, gel band protein identification, immunoprecipitation, pulldown proteomics, cleavable cross-linking mass spectrometry, |
is listed by: ABRF CoreMarketplace has parent organization: University of Miami; Florida; USA |
NCI P30CA240139 | ABRF_5972 | https://coremarketplace.org/RRID:SCR_028491/?citation=1 | SCR_028491 | , Sylvester Comprehensive Cancer Center (Sylvester) Cancer Proteomics Shared Resource (CPSR) at the University of Miami Miller School of Medicine, Sylvester Cancer Proteomics Shared Resource | 2026-08-03 09:39:34 | 0 | |||||||
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Wayne State University Microscopy Imaging and Cytometry Resources MICR Core Facility Resource Report Resource Website |
Wayne State University Microscopy Imaging and Cytometry Resources MICR Core Facility (RRID:SCR_028700) | service resource, access service resource, core facility | Core provides advanced instrumentation, consultation, and support for flow cytometry, light and electron microscopy, and small-animal imaging. Services include confocal microscopy, multi-plex whole slide imaging, conventional, widefield epifluorescence microscopy, Electron Microscopy, in vivo small animal PET, SPECT, CT, X-Ray, white light, fluorescence, and bioluminescence imaging, in vitro and in vivo X-Ray irradiation, multi-parameter flow cytometry, including conventional and spectral technologies, cell sorting, imaging cytometry, and advanced data analysis support. | ABRF, imaging services, cytometry services, microscopy services, confocal microscopy, electron microscopy, flow cytometry, cell sorting, spatial proteomics, |
is listed by: ABRF CoreMarketplace has parent organization: Wayne State University; Michigan; USA |
NCI P30 CA22453 | Open | ABRF_6044 | https://coremarketplace.org/RRID:SCR_028700/?citation=1 | SCR_028700 | , MICR Core, Wayne State University MICR Core | 2026-08-03 09:39:28 | 0 | ||||||
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HLAthena Resource Report Resource Website |
HLAthena (RRID:SCR_028691) | software resource, web application | Web tool and predictive model used by researchers to identify which small protein fragments (peptides) will be presented by human leukocyte antigen (HLA) proteins on the surface of cells. It is heavily used in the development of cancer immunotherapies and personalized | HLA-I presentation prediction, identify small protein fragments, human leukocyte antigen (HLA) proteins, surface of cells, | NCI RO1CA155010; NHLBI R01HL103532; NCI U24 CA224331; NCI R21 CA216772; NHGRI T32HG002295; NCI 5T32CA009172; NCI U24-CA210986; NCI U01 CA214125 |
PMID:31844290 | Free, Freely available | SCR_028691 | 2026-08-03 09:39:38 | 0 |
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