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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-03 05:11:41 | 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 | 2026-09-03 05:11:44 | 10 | ||||||||
|
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 | 2026-09-03 05:11:09 | 0 | ||||||||
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SigProfilerAssignment Resource Report Resource Website 10+ mentions |
SigProfilerAssignment (RRID:SCR_026899) | software application, software resource, 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 ; NCI R01CA269919; NIEHS R01ES030993; NIEHS R01ES032547; Packard Fellowship for Science and Engineering |
PMID:37502962 | Free, Available for download, Freely available, | SCR_026899 | 2026-09-03 05:10:33 | 12 | |||||||||
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signifinder Resource Report Resource Website |
signifinder (RRID:SCR_027141) | software resource, software toolkit | Software R package designed to streamline collection and use of cancer transcriptional signatures across bulk, single-cell, and spatial transcriptomics data. Used for collection and implementation of public transcriptional cancer signatures. | Collection and implementation of public transcriptional cancer signatures, transcriptional cancer signatures, transcriptomics data, | Chan Zuckerberg Initiative ; Italian Association for Cancer Research ; NCI U24CA180996 |
PMID:39363890 | Free, Available for download, Freely available | https://github.com/CaluraLab/signifinder | SCR_027141 | 2026-09-03 05:11:32 | 0 | ||||||||
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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 | 2026-09-03 05:11:24 | 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 | 2026-09-03 05:11:35 | 1 | ||||||
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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 | 2026-09-03 05:12:26 | 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 | 2026-09-03 05:12:48 | 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 | 2026-09-03 05:12:33 | 0 | |||||||||
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multiMiR Resource Report Resource Website |
multiMiR (RRID:SCR_028726) | software resource, software toolkit, source code | Software R package to integrate and query microRNA (miRNA) data. It allows retrieve and analyze validated and predicted miRNA-target interactions, as well as their associations with various diseases and drugs. | integrate and query microRNA data, retrieve and analyze validated and predicted miRNA-target interactions, diseases, drugs | NCI R01CA075115; NIAAA K01AA16922; NIAAA R01AA016957; NIAAA R01AA021131; NIAAA R24AA013162 |
PMID:25063298 | Free, Available for download, Freely available | https://github.com/KechrisLab/multiMiR, https://bioconductor.org/packages/release/bioc/html/multiMiR.html | SCR_028726 | multiMiR R package | 2026-09-03 05:12:28 | 0 | |||||||
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MARIA Resource Report Resource Website |
MARIA (RRID:SCR_028673) | software resource, web application | Web multimodal recurrent neural network tool designed to predict HLA-II (Human Leukocyte Antigen class II) peptide ligand presentation. It uses cell HLA alleles, peptide sequences, and source genes to evaluate antigen presentation. Used for predicting the likelihood of antigen presentation from a gene of interest in the context of specific HLA class II alleles. | multimodal recurrent neural network, predicting likelihood of antigen presentation, gene of interest, specific HLA class II alleles, | is organization facet of: Stanford University; Stanford; California | NCI K08 CA207882; NCI U01 CA194389; NCRR S10RR027431; NIGMS GM 102365 |
PMID:31611695 | Free, Freely available | SCR_028673 | MARIA:Major Histocompatibility Complex Analysis with Recurrent Integrated Architecture | 2026-09-03 05:12:40 | 0 | |||||||
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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 | 2026-09-03 05:08:38 | 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 | 2026-09-03 05:09:17 | 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 | 2026-09-03 05:08:47 | 26 | ||||||
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University of California at San Diego Institute for Genomic Medicine Genomics Center Core Facilitiy Resource Report Resource Website 1+ mentions |
University of California at San Diego Institute for Genomic Medicine Genomics Center Core Facilitiy (RRID:SCR_022740) | access service resource, core facility, service resource | Provides services including sequencing library preparation and sequencing on Illumina MiSeq and NovaSeq 6000 platforms. Supports single cell sequencing on 10X Genomics Chromium Controller. Provides Illumina Infinium Beadchips, which includes variety of whole genome genotyping arrays as well as Infinium MethylationEPIC BeadChip. | USEDit, ABRF, sequencing library preparation, sequencing, single cell sequencing, whole genome genotyping arrays |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of California at San Diego; California; USA |
NCI P30CA023100; NIDDK P30DK063491; NIDDK P30DK120515; NIH Office of the Director S10 OD026929 |
ABRF_1025 | https://coremarketplace.org/?FacilityID=1025&citation=1 | SCR_022740 | UCSD IGM Genomics Center | 2026-09-03 05:09:23 | 2 | |||||||
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University of California Davis Health Immune Modeling, Analysis and Diagnostics Shared Resource Core Facility Resource Report Resource Website |
University of California Davis Health Immune Modeling, Analysis and Diagnostics Shared Resource Core Facility (RRID:SCR_023587) | IMADSR | access service resource, core facility, service resource | Clinical Laboratory Improvement Amendments certified laboratory established to provide scientific support to investigators conducting clinical studies in humans, preclinical studies in animals and/or studies in veterinary medicine. Conducts immunology based assays needed to monitor patients in clinical immunotherapy trials. Offers molecular and cellular assays for investigators in different fields, including custom assays designes. | USEDit, ABRF, Clinical Laboratory Improvement Amendments certified, clinical studies in humans, preclinical studies in animals, veterinary medicine studies, immunology based assays, |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of California at Davis; California; USA |
NCI P30CA093373 | Open | ABRF_1770 | https://coremarketplace.org/?FacilityID=1770&citation=1 | SCR_023587 | UC Davis Immune Modeling, University of California, Analysis and Diagnostics Shared Resource, Davis UC Davis Immune Modeling | 2026-09-03 05:08:58 | 0 | |||||
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University of California Davis Health Genomics Shared Resource Core Facility Resource Report Resource Website |
University of California Davis Health Genomics Shared Resource Core Facility (RRID:SCR_023586) | GSR | access service resource, core facility, service resource | Provides expertise and comprehensive services to accomplish virtually every application of next generation sequencing based genomics research, including gene expression profiling, mutation/variant analyses, copy number analysis, epigenomics, metagenomics, single cell sequencing and spatial transcriptomics services. GSR also specializes in development of custom protocols and extensive data analysis and integrative bioinformatics support. The shared resource provides wide range of additional services for translational and clinical genomics research. | USEDit, ABRF, next generation sequencing based genomics research, gene expression profiling, mutation/variant analyses, copy number analysis, epigenomics, metagenomics, single cell sequencing and spatial transcriptomics services, |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of California at Davis; California; USA |
NCI P30CA093373 | ABRF_1769 | https://coremarketplace.org/?FacilityID=1769&citation=1 | SCR_023586 | UC Davis Genomics Shared Resource, University of California, Davis UC Davis Genomics Shared Resource | 2026-09-03 05:08:28 | 0 | ||||||
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University of California Davis Health Biorepository Shared Resource Core Facility Resource Report Resource Website 1+ mentions |
University of California Davis Health Biorepository Shared Resource Core Facility (RRID:SCR_023583) | BRSR | access service resource, core facility, service resource | Provides specimens with annotated data for clinical and basic science research purposes.Biorepository functions as centralized tissue bank to provide researchers access to cancer- and non-cancer-related specimens including fresh or frozen tissue, paraffin blocks,sections and fluids, procured and stored using international standards of best practices and protocols compliant with Office for Human Research Protection. Specimens can be obtained prospectively as part of clinical trials or accessed through UC Davis Health Clinical Laboratories, where over 5.5 million blood specimens are processed annually. | USEDit, ABRF, clinical and basic science research, specimens with annotated data, biorepository, tissue bank, cancer- and non-cancer-related specimens, |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of California at Davis; California; USA |
NCI P30CA093373 | ABRF_1765 | https://coremarketplace.org/?FacilityID=1765&citation=1 | SCR_023583 | UC Davis Biorepository Shared Resource, University of California Davis Health Biorepository Shared Resource | 2026-09-03 05:08:28 | 1 | ||||||
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University of California Davis Health In Vivo Translational Imaging Shared Resource Core Facility Resource Report Resource Website |
University of California Davis Health In Vivo Translational Imaging Shared Resource Core Facility (RRID:SCR_023589) | IVTISR | access service resource, core facility, service resource | Provides access to in vivo imaging technologies including molecular imaging, optical imaging, quantitative physiologic and anatomic imaging, and whole body PET/CT scanning in humans and animals. Provides targeted imaging probes and tracers as well as expertise in planning, executing and analyzing in vivo imaging studies. Supports imaging studies in small animals, large animals and humans.This resource is located in three adjacent buildings in the Health Sciences district of the Davis campus:Center for Molecular and Genomic Imaging (CMGI), Genome and Biomedical Sciences Facility (small-animal imaging);Nuclear Magnetic Resonance (NMR) Facility, Tupper Hall (small-animal MRI);Center for Imaging Sciences (CIS), Veterinary School (large-animal imaging). | USEDit, ABRF, vivo imaging technologies, molecular imaging, optical imaging, quantitative physiologic and anatomic imaging, whole body PET/CT scanning, |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of California at Davis; California; USA |
NCI P30CA093373 | ABRF_1772 | https://coremarketplace.org/?FacilityID=1772&citation=1 | SCR_023589 | University of California, Davis UC Davis In Vivo Translational Imaging Shared Resource, UC Davis In Vivo Translational Imaging Shared Resource | 2026-09-03 05:08:49 | 0 |
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