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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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University of Chicago Functional Genomics Core Facility Resource Report Resource Website 50+ mentions |
University of Chicago Functional Genomics Core Facility (RRID:SCR_019196) | access service resource, core facility, service resource | Facility offers Next-Gen Illumina and Pacific Biosciences Sequencing and Library prep services, Micro-array Illumina genotyping and EPIC arrays services, Sanger DNA Sequencing, and Bioanalyzer/Fragment analyzer sample QC services. For Single Cell sequencing project Facility operates DROP-SEQ and 10X Genomics instrument., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | USEDit, genomics, sequencing, genotyping, sample QC service, ABRF, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: University of Chicago; Illinois; USA |
NCI P30 CA014599 | THIS RESOURCE IS NO LONGER IN SERVICE | ABRF_1082 | https://coremarketplace.org/?FacilityID=1082 | SCR_019196 | Functional Genomics | 2026-09-12 01:04:09 | 91 | ||||||
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New York University Grossman School of Medicine Applied Bioinformatics Laboratories Facility Resource Report Resource Website 10+ mentions |
New York University Grossman School of Medicine Applied Bioinformatics Laboratories Facility (RRID:SCR_019178) | access service resource, core facility, service resource | Core provides computational analysis for high throughput genomic data, including but not limited to, next generation sequencing data. Our mission is to accelerate scientific discoveries by guiding experimental design, performing robust data quality assessment, and carrying out comprehensive computational analyses. Registration to iLab required. | USEDit, next generation sequencing data, genomic data, data quality assessment, computational analyses, ABRF, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: New York University School of Medicine; New York; USA |
NCI P30CA016087; NIH Office of the Director S10 OD010751 |
ABRF_819 | https://coremarketplace.org/?FacilityID=819 | SCR_019178 | Applied Bioinformatics Laboratories | 2026-09-12 01:04:09 | 10 | |||||||
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University of Colorado Anschutz Medical Campus Cancer Center Biostatistics Core Facility Resource Report Resource Website 1+ mentions |
University of Colorado Anschutz Medical Campus Cancer Center Biostatistics Core Facility (RRID:SCR_021981) | BiostatisticsBBSR | access service resource, core facility, service resource | Biostatistics provides quantitative support for planning, design, analysis, and presentation of basic science, clinical, and epidemiological investigations. We are dedicated to delivering high quality, methodically developed results to improve patient outcomes and clinical care. | ABRF, USEDit |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Colorado School of Medicine; Colorado; USA |
NCI P30CA046934 | ABRF_1306 | https://coremarketplace.org/?FacilityID=1306 | SCR_021981 | Bioinformatics - Biostatistics and Bioinformatics Shared Resource | 2026-09-12 01:04:13 | 6 | ||||||
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Cold Spring Harbor Laboratory Flow Cytometry Shared Resource Core Facility Resource Report Resource Website 1+ mentions |
Cold Spring Harbor Laboratory Flow Cytometry Shared Resource Core Facility (RRID:SCR_022164) | CSHL | access service resource, core facility, service resource | Resource provides equipment, training, and operating assistance for cell sorting and analysis. Facility staff oversees equipment maintenance, trains new users, and assists with assay development and operation of equipment. | USEDit, ABRF, flow cytometry |
is listed by: ABRF CoreMarketplace is related to: USEDit |
NCI | open | ABRF_1336 | https://coremarketplace.org/?FacilityID=1336 | SCR_022164 | CSHL - Flow Cytometry Shared Resource, Cold Spring Harbor Laboratory Flow Cytometry Shared Resource | 2026-09-12 01:04:14 | 2 | |||||
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University of Pennsylvania Perelman School of Medicine Cytomics and Cell Sorting Resource Laboratory Core Facility Resource Report Resource Website 50+ mentions |
University of Pennsylvania Perelman School of Medicine Cytomics and Cell Sorting Resource Laboratory Core Facility (RRID:SCR_022376) | access service resource, core facility, service resource | Flow cytometry shared resource laboratory at the University of Pennsylvania. Facility has instruments, which include analyzers, cell sorters, small particle detectors, dual fluorescence cell counter/viability instrument, tissue dissociator for cell preparation. Provides on-site and off-site support to instrument users, including analyzer and cell sorter training. Core's Research and Development team collaborates/consults with principal investigators in developing high-dimensional panels, as well as staining, acquisition, and analysis. | ABRF, flow cytometry, cell sorting, analyzer and cell sorter training, |
is listed by: ABRF CoreMarketplace has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
NCI P30 016520 | Open | ARBF_1389 | https://coremarketplace.org?citation=1&FacilityID=1389 | SCR_022376 | Penn Cytomics, Cytomics and Cell Sorting Resource Laboratory, University of Pennsylvania Perelman School of Medicine Cytomics and Cell Sorting Resource Laboratory | 2026-09-12 01:04:16 | 79 | ||||||
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University of Miami Sylvester Onco Genomics Shared Resource Core Facility Resource Report Resource Website 10+ mentions |
University of Miami Sylvester Onco Genomics Shared Resource Core Facility (RRID:SCR_022502) | OGSR | access service resource, core facility, service resource | Provides access to technologies and services for study of genomics and epigenomics of cancer, in addition to providing technical expertise for project design, trouble shooting and pre and post award support. Services include next generation sequencing, single cell genomics, spatial genomics, gene expression assays and molecular quantitation, services for sample extraction and QC. | USEDit, ABRF, cancer genomics and epigenomics, next generation sequencing, single cell genomics, spatial genomics, gene expression assays, molecular quantitation, sample extraction and QC |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Miami; Florida; USA |
NCI CA240139 | ABRF_1463 | https://coremarketplace.org/?FacilityID=1463&citation=1 | SCR_022502 | UM Sylvester Onco-Genomics Shared Resource, University of Miami UM Sylvester Onco-Genomics Shared Resource | 2026-09-12 01:04:18 | 26 | ||||||
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CLEAR Resource Report Resource Website 1+ mentions |
CLEAR (RRID:SCR_027171) | software resource, software toolkit, 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 | 2026-09-12 01:05:20 | 1 | ||||||||
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RAIDS (Robust Ancestry Inference using Data Synthesis) Resource Report Resource Website 1+ mentions |
RAIDS (Robust Ancestry Inference using Data Synthesis) (RRID:SCR_027265) | RAIDS | data analysis software, data processing software, simulation software, software application, 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 P20CA192996; NCI P30CA45508; NCI R01CA188134; NCI R01CA229699; NCI R01CA249002; NCI U01CA210240; NCI U01CA224013 |
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 | 2026-09-12 01:05:23 | 1 | ||||||
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SEAHORSE Resource Report Resource Website 1+ mentions |
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; NCI U24 CA231846; NHGRI R01 HG011393 |
DOI:10.1101/2025.08.15.670514v1 | Free, Freely available, | SCR_027399 | Serendipity Engine Assaying Heterogeneous Omics Related Sampling Experiments | 2026-09-12 01:05:26 | 1 | ||||||||
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GenVisR Resource Report Resource Website 10+ mentions |
GenVisR (RRID:SCR_027559) | software resource, software toolkit | Software R package for visualizing genomics data. Provides a user-friendly, flexible and comprehensive suite of tools for visualizing complex genomic data in three categories (small variants, copy number alterations and data quality) for multiple species of interest. | visualizing genomics data, genomics, genomics data, small variants, copy number alterations, data quality, multiple species, | NCI K22CA188163; NHGRI K99HG007940 |
PMID:27288499 | Free, Available for download, Freely available | SCR_027559 | 2026-09-12 01:05:30 | 42 | |||||||||
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BayesPrism Resource Report Resource Website 10+ mentions |
BayesPrism (RRID:SCR_027499) | software resource, software toolkit, 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, | NCI U2C CA288284; NCI U54 CA209975; NHGRI R01 HG009309 |
PMID:35469013 | Free, Available for download, Freely available | SCR_027499 | 2026-09-12 01:05:28 | 14 | |||||||||
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CytoSPACE Resource Report Resource Website 10+ mentions |
CytoSPACE (RRID:SCR_027634) | software application, software resource, 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 ; Donald E. and Delia B. Baxter Foundation ; NCI R00CA187192; NCI R01CA255450; NCI R21CA238971; Norwegian Cancer Society ; Virginia and D. K. Ludwig Fund for Cancer Research |
PMID:36879008 | Free, Available for download, Freely available | https://github.com/digitalcytometry/cytospace | SCR_027634 | 2026-09-12 01:05:32 | 10 | ||||||||
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METAFlux Resource Report Resource Website 1+ mentions |
METAFlux (RRID:SCR_028022) | software application, software resource, 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, | Chan Zuckerberg Initiative ; MD Anderson Moonshot programs ; NCI P30 CA016672; NCI U01CA247760; Silicon Valley Community Foundation |
PMID:37573313 | Free, Available for download, Freely available | SCR_028022 | 2026-09-12 01:05:41 | 6 | |||||||||
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BISCUIT Resource Report Resource Website 1+ mentions |
BISCUIT (RRID:SCR_028006) | software resource, software toolkit | Software application for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Used to perform alignment, DNA methylation and mutation calling, and allele specific methylation from bisulfite sequencing data. Analyzing sodium bisulfite conversion-based DNA methylation/modification data. | simultaneous genetic and epigenetic inference, analyzing sodium bisulfite conversion-based DNA methylation/modification data, perform alignment, DNA methylation, mutation calling, allele specific methylation, bisulfite sequencing data, | NCI R37CA230748; NCI U24CA264023; NIGMS R35GM146978 |
PMID:38412294 | Free, Available for download, Freely available | SCR_028006 | , BISulfite-seq CUI Toolkit, BISulfite-seq CUI Toolkit (BISCUIT) | 2026-09-12 01:05:41 | 2 | ||||||||
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CivicDb Resource Report Resource Website 1+ mentions |
CivicDb (RRID:SCR_028055) | data or information resource, database, knowledge base | 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 | NCATS UL1TR002345; NCI K22CA188163; NCI U01CA209936; NCI U24CA237719; NHGRI R00HG007940; NHGRI R00HG010157; NHGRI U41 HG008735 |
PMID:36373660 | Free, Freely available, | SCR_028055 | , Clinical Interpretation of Variants in Cancer, CIViCdb | 2026-09-12 01:05:42 | 5 | |||||||
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EpiProfile Resource Report Resource Website |
EpiProfile (RRID:SCR_028224) | software application, software resource, 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, | NCATS TL1TR001880; NCI CA196539; NIAID AI118891; NIGMS GM110174; NIGMS T32GM008275; UPenn Epigenetics Institute |
PMID:25805797 PMID:29790754 |
Free, Available for download, Freely available | SCR_028224 | EpiProfile 2.0 | 2026-09-12 01:05:46 | 0 | ||||||||
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HiTAIC Resource Report Resource Website |
HiTAIC (RRID:SCR_028181) | data access protocol, software resource, web service | 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, | NCI P30CA023108; NCI R01CA216265; NCI R01CA253976; NCI R01CA275974; NIGMS P20GM104416 |
PMID:37089814 | Free, Freely available | SCR_028181 | Hierarchical Tumor Artificial Intelligence Classifier | 2026-09-12 01:05:45 | 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) | access service resource, core facility, service resource | 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 | 2026-09-12 01:05:52 | 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) | access service resource, core facility, service resource | 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 | 2026-09-12 01:05:57 | 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 5T32CA009172; NCI R21 CA216772; NCI RO1CA155010; NCI U01 CA214125; NCI U24 CA224331; NCI U24-CA210986; NHGRI T32HG002295; NHLBI R01HL103532 |
PMID:31844290 | Free, Freely available | SCR_028691 | 2026-09-12 01:05:57 | 0 |
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