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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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scRepertoire Resource Report Resource Website 50+ mentions |
scRepertoire (RRID:SCR_025691) | software resource, software toolkit | Software R toolkit for analyzing single-cell immune repertoire profiling. Used for single-cell immune receptor analysis. | single-cell immune receptor analysis, single-cell immune repertoire profiling, | NCI CA206255 | PMID:32789006 | Free, Available for download, Freely available | https://bioconductor.org/packages/release/bioc/html/scRepertoire.html | SCR_025691 | 2026-09-12 01:04:50 | 87 | ||||||||
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NovoBreak Resource Report Resource Website 1+ mentions |
NovoBreak (RRID:SCR_026032) | software application, software resource, source code | Software tool to discover somatic and germline structural variation breakpoints in whole genome sequencing data. Can report accurate breakpoints of Deletions, Duplications, Inversions and Translocations. Designed for Illumina paired-end data. Local assembly for breakpoint detection in cancer genomes. | discover somatic and germline structural variation, structural variation breakpoints, whole-genome sequencing data, local assembly, breakpoint detection, cancer genomes, | NCI P30 CA016672; NCI R01 CA172652; NHGRI U41 HG007497 |
PMID:27892959 | Free, Available for download, Freely available, | SCR_026032 | 2026-09-12 01:04:56 | 2 | |||||||||
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UpSetR Resource Report Resource Website 50+ mentions |
UpSetR (RRID:SCR_026112) | software resource, software toolkit, source code | Software R package for visualization of intersecting sets and their properties. | visualization of intersecting sets, | NCI U01 CA198935; NHGRI R00 HG007583; NHGRI U54HG007963 |
PMID:28645171 | Free, Available for download, Freely available | https://cran.rstudio.com/web/packages/UpSetR/ | SCR_026112 | 2026-09-12 01:04:57 | 89 | ||||||||
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AutoGVP Resource Report Resource Website 1+ mentions |
AutoGVP (RRID:SCR_026107) | software application, software resource, source code | Software tool integrates ClinVar variant annotation with modified InterVar classification approach, based on American College of Medical Genetics-Association for Molecular Pathology guidelines, to output germline variant classification. Since AutoGVP input only requires VCF file, it can facilitate large-scale, clinically focused classification of germline sequence variants. | germline variant classification, germline sequence variants, germline, sequence variants, | is related to: ClinVar | NCI R01CA237562; NCI R03CA230366; NCI R03CA287169 |
PMID:38426335 | Free, Available for download, Freely available | SCR_026107 | Automated Germline Variant Pathogenicity | 2026-09-12 01:04:57 | 3 | |||||||
|
OncoTree Resource Report Resource Website 10+ mentions |
OncoTree (RRID:SCR_026218) | data or information resource, disease-related portal, portal, topical portal | Community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research. Cancer classification system for precision oncology. | cancer classification platform, rare and common cancers, cancer classification, precision oncology, | cancer | NCI P30 CA008748 | PMID:33625877 | Free, Freely available | SCR_026218 | 2026-09-12 01:05:00 | 20 | ||||||||
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AACR GENIE cBioPortal Resource Report Resource Website 10+ mentions |
AACR GENIE cBioPortal (RRID:SCR_026217) | consortium, data or information resource, organization portal, 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, | Howard Hughes Medical Institute ; NCI 2P30CA006516; NCI 5P30CA068485; NCI 5P50CA083639; NCI 5P50CA098258; NCI 5U01CA168394; NCI CA006973; NCI CA008748; NCI CA121113; NCI CA180950; NCI U24CA209851; NCI U24CA210950; NHGRI U54HG008100 |
PMID:28572459 | Restricted | SCR_026217 | 2026-09-12 01:05:00 | 26 | |||||||||
|
CRAPome Resource Report Resource Website 10+ mentions |
CRAPome (RRID:SCR_025008) | data access protocol, data or information resource, database, software resource, web service | Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions. | Mass Spectrometry contaminants, standardized negative controls, contaminant repository, AP-MS analysis, affinity purification, mass spectrometry data, | Austrian Academy of Sciences ; Austrian Federal Ministry for Science and Research ; Austrian Science Fund ; Canadian Institutes of Health Research ; European Molecular Biology Organisation ; European Research Council ; European Union 7th Framework Program ; government of Ontario ; Human Frontier Science Program ; NCI R21 CA16006001A1; Netherlands Proteomics Center ; NHLBI HL112618-01; NIDA DP1DA026192; NIGMS 5R01GM94231; Stowers Institute for Medical Research |
PMID:23921808 | Free, Freely available, | https://reprint-apms.org/ | SCR_025008 | CRAPome:Contaminant Repository for Affinity Purification | 2026-09-12 01:04:35 | 24 | |||||||
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ReDU Resource Report Resource Website 1+ mentions |
ReDU (RRID:SCR_025105) | data access protocol, software resource, web service | Software framework to find and re-analyze public Mass Spectrometry data. Used to find uniformly formatted public MS/MS data in the Global Natural Product Social Molecular Networking Platform (GNPS) via formatted metadata. New or previously collected data can be added provided they adhere to the ReDU metadata standards (the implemented drag-and-drop validator is applicable to any scientific data) and data are available in GNPS/MassIVE. | Mass Spectrometry data, find uniformly formatted public MS/MS data, formatted metadata, Global Natural Product Social Molecular Networking Platform, GNPS, find and re-analyze public Mass Spectrometry data, ReDU metadata standards, data validator, | has parent organization: University of California at San Diego; California; USA | American Society for Mass Spectrometry ; FAPESP ; Gordon and Betty Moore Foundation ; Krupp Endowed Fund ; NCI R03 CA211211; Netherlands eScience Center ; NIGMS P41 GM103484; NIGMS R01 GM107550; NSF ; Sloan Foundation ; University of California ; San Diego Center for Microbiome Innovation SEED grants ; US Office of Naval Research |
PMID:32807955 | Free, Freely available | SCR_025105 | Reanalysis of Data User | 2026-09-12 01:04:37 | 2 | |||||||
|
IBEX Knowledge Base Resource Report Resource Website 1+ mentions |
IBEX Knowledge Base (RRID:SCR_025296) | knowledge base | Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase. | Antibody, validation, multiplexed imaging, | Chan Zuckerberg Initiative ; NCI ; NIAID ; Schroeder Allergy and Immunology Research Institute ; McMaster University ; CA ; Wellcome Trust |
Free, Freely available | https://zenodo.org/records/7693279 | SCR_025296 | Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base | 2026-09-12 01:04:41 | 4 | ||||||||
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TooManyCells Resource Report Resource Website 1+ mentions |
TooManyCells (RRID:SCR_025328) | software resource, software toolkit, source code | Software suite of tools, algorithms, and visualizations focusing on relationships between cell clades. This includes new ways of clustering, plotting, choosing differential expression comparisons. Identifies and visualizes relationships of single-cell clades. | Spectral clustering, radial tree, visualization, cell clades, |
is related to: too-many-cells-python is related to: TooManyCellsInteractive |
NCI R01 CA215518; NCI R01 CA230800; NCI T32 CA009140; NHLBI R01 HL145754; Sloan Foundation |
PMID:32123397 | Free, Available for download, Freely available | https://gregoryschwartz.github.io/too-many-cells/ | SCR_025328 | 2026-09-12 01:04:42 | 4 | |||||||
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glmpca Resource Report Resource Website 1+ mentions |
glmpca (RRID:SCR_025517) | software resource, software toolkit, source code | Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data. | dimension reduction, non-normally distributed data, principal components analysis, | Chan-Zuckerberg Initiative ; NCI T32CA009337; NHGRI P41HG004059; NHGRI R00HG009007; NHGRI R01HG005220; NIGMS R01GM083084 |
PMID:31870412 | Free, Available for download, Freely available, | https://CRAN.R-project.org/package=glmpca | SCR_025517 | generalized version of principal components analysis | 2026-09-12 01:04:46 | 2 | |||||||
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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 | |||||||
|
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 | ||||||
|
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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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 | 2026-09-12 01:05:58 | 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 | 2026-09-12 01:05:57 | 0 | |||||||
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Memorial Sloan Kettering Cancer Center Antibody and Bioresource Core Facility Resource Report Resource Website 1+ mentions |
Memorial Sloan Kettering Cancer Center Antibody and Bioresource Core Facility (RRID:SCR_017691) | ABCF | access service resource, core facility, service resource | ABCF can provide MAbs from established hybridomas for RESEARCH PURPOSES ONLY, can assist in generating MAbs, offers a weekly mycoplasmal contamination screening service for tissue culture samples, distributes cell lines developed at Memorial Sloan Kettering Cancer Center and Rockefeller University. | Monoclonal, antibody, hybridoma, mycoplasma, screening, service, tissue, culture, sample, cell, line, core |
is listed by: ABRF CoreMarketplace has parent organization: Memorial Sloan Kettering Cancer Center |
NCI P30 CA008748 | Restricted | SCR_017709, ABRF_51 | https://ilab.mskcc.org/service_center/show_external/3451, https://coremarketplace.org/?FacilityID=85 | SCR_017691 | Antibody and Bioresource Core Facility | 2026-09-12 01:04:00 | 2 | |||||
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Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility Resource Report Resource Website 100+ mentions |
Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility (RRID:SCR_017801) | access service resource, core facility, service resource | Core mass spec and proteomic services include open access lab for trained users with GC/MS, LC/MS, high resolution LC/MS, and MALDI-TOF instruments, help with intact protein analysis, targeted quantitation, drug discovery support, pathway analysis, protein interactions, FFPE tissue analysis, both labeled and label-free proteomics, and more. Please contact SUMS to discuss these and other custom projects including new application development. | Mass, spectrometry, proteomics, training, analysis, targeted, quantitation, drug, discovery, pathway, protein, interaction, service, USEDit, ABRF |
uses: Waters: SQD2 LC/MS system uses: Waters: Select Series Cyclic IMS uses: Thermo Fisher: Exactive Orbitrap LC/MS system uses: Thermo Fisher: LTQ XL LC/MS system uses: Thermo Fisher: Orbitrap Fusion nanoLC/MS system uses: Thermo Fisher: QE-HFX mass spectrometer uses: Thermo Fisher: Vantage LC/MS mass spectrometer uses: Stanford Sciex 7500+ Triple Quadrupole LC/MS system uses: Waters: Quattro Premier LC/MS system uses: Stanford Shimadzu 8030 LC/MS mass spectrometer uses: Bruker: Scion TQ GC/MS mass spectrometer uses: Bruker: micrOTOF-Q II LC/MS system uses: Agilent: 7890/5975 GC/MS system uses: Thermo Fisher: Orbitrap Eclipse nanoLC/MS system uses: Thermo Fisher: Exploris 480 nanoLC/MS system uses: Thermo Fisher: Exploris 240 LC/MS system uses: Waters: Andrew Pipetting Robot uses: Agilent: 6495 Triple Quadrupole LC/MS uses: Waters: Select Series MRT uses: Stanford Bruker timsTOF Ultra nanoLC/MS uses: Thermo Fisher: LTQ-Orbitrap Elite nano LC/MS system uses: Bruker: Microflex MALDI TOF mass spectrometer uses: Waters: Xevo TQ-XS mass spectrometer is listed by: ABRF CoreMarketplace has parent organization: Stanford University; Stanford; California |
NCI CA124435; NIH S10 OD026962; NIH S10 RR027425; Vincent and Stella Coates |
Open | ABRF_489 | https://coremarketplace.org/?FacilityID=489 | SCR_017801 | Vincent Coates Foundation Mass Spectrometry Laboratory | 2026-09-12 01:04:02 | 117 | ||||||
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Northwestern University Cancer Center Flow Cytometry Core Facility Resource Report Resource Website |
Northwestern University Cancer Center Flow Cytometry Core Facility (RRID:SCR_017766) | access service resource, core facility, service resource | Provides 6 cell sorters and 5 benchtop analyzers. Helps investigators to define their projects in the early stages of development to make optimal and efficient use of flow cytometry. Educates ALL users (faculty and staff) in the science and technology of flow cytometry. | Flow, cytometry, analysis, training, service, core | NCI CA060553; NIH Office of the Director S10 OD011996 |
Restricted | ABRF_315 | SCR_017766 | Robert H. Lurie Comprehensive Cancer Center Flow Cytometry Core Facility | 2026-09-12 01:04:01 | 0 | ||||||||
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Northwestern University School of Medicine Lurie Cancer Center Pathology Core Facility Resource Report Resource Website 1+ mentions |
Northwestern University School of Medicine Lurie Cancer Center Pathology Core Facility (RRID:SCR_017769) | PCF | access service resource, core facility, service resource | Centralized, comprehensive, core laboratory providing histology, immunohistochemistry, molecular analysis and extraction and microscopic evaluation services for human tissue-based studies. Serves integral marker studies that require biomarker-based treatment arm assignment. Performs procurement of fresh biospecimens for clinical trials and biobanking. | Pathology, histology, immunohistochemistry, molecular, analysis, extraction, microscopic, evaluation, human, tissue, biobanking, service, core | NCI CA060553 | ABRF_333 | SCR_017769 | Pathology Core Facility | 2026-09-12 01:04:01 | 3 |
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