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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MRQy Resource Report Resource Website 1+ mentions |
MRQy (RRID:SCR_025779) | data analysis software, data processing software, software application, software resource | Software quality assurance and checking tool for quantitative assessment of magnetic resonance imaging and computed tomography data. Used for quality control of MR imaging data. | quantitative assessment, magnetic resonance imaging, computed tomography, imaging data, | NCI 1F31CA216935; NCI 1U01CA239055; NCI 1U01CA248226; NCI R01CA202752; NCI R01CA208236; NCI R01CA216579; NCI R01CA220581; NCI U24CA199374; NCRR 1C06RR12463; NHLBI R01HL15127701A1; NIBIB 1R43EB028736 |
PMID:33176026 | Free, Available for download, Freely available | SCR_025779 | 2026-08-29 11:34:12 | 1 | |||||||||
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tximeta Resource Report Resource Website 1+ mentions |
tximeta (RRID:SCR_028005) | software resource, software toolkit | Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility. | reference sequence checksums, provenance identification in RNA-seq, numerous annotation, metadata gathering, | NCI P01 CA142538; NHGRI R01 HG009937; NHGRI U41 HG004059; NIEHS P30 ES010126; NIMH R01 MH118349 |
PMID:32097405 | Free, Available for download, Freely available | SCR_028005 | Tximeta | 2026-08-29 11:35:40 | 1 | ||||||||
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HiTIMED Resource Report Resource Website |
HiTIMED (RRID:SCR_028180) | software application, software resource, source code | Software DNA methylation-based algorithm, to estimate cell proportions in tumor microenvironment. Profiles tumor, immune, and angiogenic components, allowing researchers to study tumor composition and its clinical implications using archival biospecimens. | estimate cell proportions, cell type resolution, tumor microenvironment, tumor-type-specific DNA methylation data, | NCI P30 CA168524; NCI P50 CA097257; NCI R01 CA207360; NCI R01CA216265; NIGMS P20 GM130423; NIGMS P20GM103428; NIGMS P20GM104416 |
PMID:36348337 | Free, Available for download, Freely available | SCR_028180 | Hierarchical Tumor Immune Microenvironment Epigenetic Deconvolution | 2026-08-29 11:35:42 | 0 | ||||||||
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somalier Resource Report Resource Website |
somalier (RRID:SCR_028167) | software application, software resource | Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches. | rapid relatedness estimation, cancer and germline studies, efficient genome sketches, quality control, | NCI P30CA04014; NCI R37CA246183; NCI U24CA209999; NHGRI R01HG009141; NHGRI R41HG010126 |
PMID:32664994 | Free, Available for download, Freely available | SCR_028167 | Somalier | 2026-08-29 11:35:37 | 0 | ||||||||
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OncoDB Resource Report Resource Website 50+ mentions |
OncoDB (RRID:SCR_028340) | data or information resource, database | Database offers integrated multi-omic data for patients across 33 cancer types. It encompasses gene expression, DNA methylation, somatic mutations, proteomic profiles, and chromatin accessibility, drawing from TCGA, GTEx, and CPTAC projects. Users can compare gene expression, DNA methylation, and protein levels between tumor and normal tissues, identifying differentially expressed genes and proteins, and examining gene-to-gene correlations. Provides oncogene mutation profiles and allows for survival analysis based on gene expression and methylation, linked to clinical parameters. Facilitates exploration of multi-omic correlations, such as gene expression with DNA methylation, and their variations with mutation status. Extends its analytical capabilities to include six major oncoviruses, offering insights into their impact on gene expression, methylation, and patient survival. | cancer patients data, gene expression, DNA methylation, somatic mutations, proteomic profiles, chromatin accessibility, | NCI R01CA287778; NIDCR R01DE026471; NIGMS R35GM141535 |
PMID:34718715 PMID:40995640 |
Free, Freely available, | SCR_028340 | OncoDB2.0 | 2026-08-29 11:35:40 | 84 | ||||||||
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BoneMarrowMap Resource Report Resource Website 1+ mentions |
BoneMarrowMap (RRID:SCR_028324) | software resource, software toolkit, source code | Software R package to enable rapid reference mapping and annotation of new scRNA-seq data across the spectrum of normal and malignant hematopoietic contexts. Single cell RNA-seq reference map of human hematopoietic development in the bone marrow, with balanced representation of hematopoietic stem and progenitor cells and differentiated populations. | bone marrow AML acute myeloid leukemia scRNA-seq, reference mapping and annotation, scRNA-seq data, hematopoietic context, reference map, human hematopoietic development, bone marrow, | NCI P30 CA021765; NCI R35 CA197695 |
PMID:40294241 | Free, Available for download, Freely available | SCR_028324 | 2026-08-29 11:35:40 | 5 | |||||||||
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MHCnuggets Resource Report Resource Website |
MHCnuggets (RRID:SCR_028674) | software application, software resource, source code | Software tool that predicts how protein pieces bind to Major Histocompatibility Complex (MHC) molecules. It uses deep learning to process peptide sequences, handle variable lengths, and evaluate both common and rare alleles. Used to predicts peptide-MHC binding. Can predict binding for common or rare alleles of MHC class I or II with a single neural network architecture. | MHC Class I and Class II neoantigen binding prediction, predict peptide-MHC binding, | Dutch Cancer Society International Translational Cancer Research ; NCI CA006973; NCI CA121113; NCI CA180950 |
PMID:31871119 | Free, Available for download, Freely available | SCR_028674 | 2026-08-29 11:35:50 | 0 | |||||||||
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University of Wisconsin-Madison Advanced Genome Editing Laboratory Resource Report Resource Website 10+ mentions |
University of Wisconsin-Madison Advanced Genome Editing Laboratory (RRID:SCR_021070) | AGEL | access service resource, core facility, service resource | Provides services and expertise to unlock genome editing tools to advance your research. Routinely generates new genome edited models, particularly mouse, rats, swine, and cell lines, as well as supports in vivo editing, novel preclinical therapeutic strategies, pooled lentiCRISPR screening, and other applications. | USEDit, generating genome edited models, mouse, rats, swine, ABRF, ABRF, CRISPR, gene editing, genome editing, lentiCRISPR |
is listed by: ABRF CoreMarketplace has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NCI P30 CA014520 | ABRF_1148 | https://coremarketplace.org/?FacilityID=1148 | SCR_021070 | University of Wisconsin Madison UW-Genome Editing & Animal Models, UW-Genome Editing & Animal Models, University of Wisconsin Madison Advanced Genome Editing Laboratory, UW Biotechnology Center Advanced Genome Editing Laboratory, Genome Editing and Animal Models Core, University of Wisconsin Madison Genome Editing Core Facility, Transgenic Animal Facility | 2026-08-29 11:33:21 | 14 | ||||||
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Memorial Sloan Kettering Cancer Center Flow Cytometry Core Facility Resource Report Resource Website 1+ mentions |
Memorial Sloan Kettering Cancer Center Flow Cytometry Core Facility (RRID:SCR_021105) | MSKCC FCCF | access service resource, core facility, service resource | Provides advanced instrumentation as well as high level technical and scientific expertise in multi dimensional Flow Cytometry and Cell Sorting, to facilitate science, improve the quality, and advance the scope of MSK research. | Flow Cytometry service, Cell Sorting service, ABRF, |
is listed by: ABRF CoreMarketplace has parent organization: Memorial Sloan Kettering Cancer Center |
NCI CA008748 | ABRF_1154 | https://coremarketplace.org/?FacilityID=1154 | SCR_021105 | Memorial Sloan Kettering Cancer Center MSKCC-FCCF, MSKCC-FCCF | 2026-08-29 11:33:21 | 2 | ||||||
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Dartmouth Geisel School of Medicine Mouse Modeling Core Facility Resource Report Resource Website |
Dartmouth Geisel School of Medicine Mouse Modeling Core Facility (RRID:SCR_021284) | access service resource, core facility, service resource | Supports generation and utilization of genetically modified mice, design and production of genetic constructs with methods including yeast and E.coli recombineering, ES cell targeting (transfection, drug selection, and expansion). Produces transgenic mice: DNA injections into oocytes, ES cell injections into blastocysts.Provides humanized immune system mouse models.Offers start to finish experiment services to assist your many needs, please ask for more info.Other services include animal husbandry, IP and IV injections, blood drawing, necropsy and surgeries- embryo transfers, ovariectomy, vasectomy, tumor removal. | ABRF, genetically modified mice, design and production of genetic constructs, |
is listed by: ABRF CoreMarketplace has parent organization: Dartmouth College; New Hampshire; USA |
NCI | restricted | ABRF_264 | https://coremarketplace.org/?FacilityID=264 | SCR_021284 | Dartmouth Mouse Modeling Shared Resource, Mouse Modeling Shared Resource | 2026-08-29 11:33:24 | 0 | ||||||
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Dartmouth Genomics and Molecular Biology Shared Resource (GMBSR) Resource Report Resource Website 50+ mentions |
Dartmouth Genomics and Molecular Biology Shared Resource (GMBSR) (RRID:SCR_021293) | access service resource, core facility, service resource | Genomics Section provides services and instrumentation that enable DNA/RNA extraction and quality control, next-generation Illumina and Nanopore sequencing, epigenetic profiling, and microarray analysis on a whole-genome scale, from the level organisms to single cells. Molecular Biology Section provides DNA fragment analysis qPCR, Sanger sequencing and NanoString Technology. | USEDit, ABRF, DNA fragment analysis qPCR, Sanger sequencing, NanoString Technology, |
is listed by: ABRF CoreMarketplace has parent organization: Dartmouth College; New Hampshire; USA |
NCI 5P30CA023108; NIGMS P20GM130454; NIH Office of the Director 1S10OD030242; NIH Office of the Director S10OD025235 |
ABRF_995 | https://coremarketplace.org/?FacilityID=995 | SCR_021293 | Molecular Biology Resource, Molecular Biology Shared Resource | 2026-08-29 11:33:24 | 62 | |||||||
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University of Chicago Human Tissue Resource Center Core Facility Resource Report Resource Website 10+ mentions |
University of Chicago Human Tissue Resource Center Core Facility (RRID:SCR_019199) | access service resource, core facility, service resource | Coordinated, centralized, and dedicated program for procuring, processing, dispersing and assessing all types of biospecimens together with downstream histology services. CAP Accredited. | USEDit, biospecimen procuring, biospecimen processing, biospecimen dispersing, biospecimen assessing, ABRF, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: University of Chicago; Illinois; USA |
NCI P30CA014599 | ABRF_1085 | https://coremarketplace.org/?FacilityID=1085 | SCR_019199 | Human Tissue Resource Center | 2026-08-29 11:33:20 | 47 | |||||||
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University of Chicago Integrated Light Microscopy Core Facility Resource Report Resource Website 50+ mentions |
University of Chicago Integrated Light Microscopy Core Facility (RRID:SCR_019197) | access service resource, core facility, service resource | Offers microscopy imaging, including bright field color and DIC, fluorescence multi-dimension,TIRFM including bleaching, ablation, FLIM and high resolution, highspeed, high sensitivity, confocal, and physiologic techniques, STED, GSD3D, lightsheet selective plane illumination and lattice lightsheet structured illumination super resolution microscopy. | USEDit, microscopy, imaging, super resolution microscopy, confocal, fluorescence, physiologic techniques, ABRF, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: University of Chicago; Illinois; USA |
NCI P30 CA014599 | ABRF_1083 | https://coremarketplace.org/?FacilityID=1083 | SCR_019197 | Integrated Light Microscopy | 2026-08-29 11:33:20 | 61 | |||||||
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New York University Grossman School of Medicine Langone Health Cytometry and Cell Sorting Laboratory Core Facility Resource Report Resource Website 10+ mentions |
New York University Grossman School of Medicine Langone Health Cytometry and Cell Sorting Laboratory Core Facility (RRID:SCR_019179) | access service resource, core facility, service resource | Provides access to flow cytometry and cell sorting technologies and instruments. If your research requires cytometric analysis, instruments acquire optical measurements using different lasers to detect fluorophores with high level of precision. | flow cytometry, cell sorting, cytometric analysis, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: New York University; New York; USA |
NCI P30CA016087 | ABRF_821 | https://coremarketplace.org/?FacilityID=821 | SCR_019179 | Cytometry and Cell Sorting Laboratory | 2026-08-29 11:33:22 | 22 | |||||||
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University of Nebraska Medical Center Advanced Microscopy Core Facility Resource Report Resource Website 10+ mentions |
University of Nebraska Medical Center Advanced Microscopy Core Facility (RRID:SCR_022467) | access service resource, core facility, service resource | Facility houses imaging technologies ranging from super resolution (~ 0.120 um to 0.020 um) to microscopic (~ 0.300 um) to mesoscopic (~ 1 um) biomedical imaging. Imaging specialists provide training and/or actively assist researchers collecting images across imaging instrumentation. Instrumentation includes Zeiss ELYRA PS.1 is inverted microscope for super resolution (SR) structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM) including, PhotoActivated Localization Microscopy (PALM) using photo switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM);Zeiss 800 CLSM with Airyscan is an inverted microscope dramatically increasing conventional confocal image resolution to ~180 nm using Airyscan technology; Zeiss 710 LSM is inverted microscope supporting most basic imaging applications, multi channel and spectral, co localization, live cell, 3D, and time series imaging; Zeiss Celldiscoverer 7 is widefield imaging system for automated, time lapse imaging of live samples; Zeiss Axioscan 7 is high performance whole slide scanning system for fluorescence, brightfield, and polarization imaging;Miltenyi Biotec Ultramicroscope II Light Sheet fluorescence microscope (LSFM) extends fluorescent imaging into true 3D, large scale volumetric imaging of intact tissues, organs, and small organisms. AMCF also houses several high-end data analysis workstations with premier image analysis software including HALO (Indica Labs) and IMARIS (Oxford Instruments) facilitating data rendering, analyses, and presentation options. | USEDit, ABRF, biomedical imaging, microscopy |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of Nebraska; Nebraska; USA |
NCI CA036727; NCRR RR027301; NIGMS GM103427; NIGMS GM106397; NIH Office of the Director OD030486 |
open | ABRF_1375 | https://coremarketplace.org/?FacilityID=1375&citation=1 | SCR_022467 | UNMC Advanced Microscopy Core Facility | 2026-08-29 11:33:15 | 23 | ||||||
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University of Texas Southwestern Medical Center Quantitative Light Microscopy Core Facility Resource Report Resource Website 1+ mentions |
University of Texas Southwestern Medical Center Quantitative Light Microscopy Core Facility (RRID:SCR_022605) | QLMC | access service resource, core facility, service resource | Provides access to variety of microscope modalities including laser scanning and spinning disk confocal, multiphoton, wide field deconvolution, CFP/YFP FRET, TIRF, single molecule imaging, and more. Offers customized microscopy training, advise and help with sample preparation, image quantification, and offer basic microscope maintenance. Can streamline your data handling and image visualization as well as automate your image analysis workflow through customized Fiji macros. | Light microscopy, laser scanning and spinning disk confocal, multiphoton, wide field deconvolution, CFP/YFP FRET, TIRF, single molecule imaging, ABRF, USEDit |
is related to: USEDit has parent organization: University of Texas Southwestern Medical Center; Texas; USA |
NCI 1P30 CA142543; NCRR 1S10 RR029731; NIH Office of the Director 1S10 OD021684; NIH Office of the Director 1S10OD028630 |
Restricted | SCR_022605 | Quantitative Light Microscopy Core | 2026-08-29 11:33:28 | 2 | |||||||
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Nationwide Children’s Hospital Abigail Wexner Research Institute Biopathology Center Core Facility Resource Report Resource Website |
Nationwide Children’s Hospital Abigail Wexner Research Institute Biopathology Center Core Facility (RRID:SCR_023260) | CHTN | access service resource, core facility, service resource | Provides services related to biospecimen procurement, banking, processing, and distribution. Housed biospecimen collections are from biorepositories of National Cancer Institute funded Children’s Oncology Group, NRG Oncology-Columbus (formerly the GOG Tissue Bank), SWOG, Pediatric Division of Cooperative Human Tissue Network, and Biospecimen Core Resource of Center for Cancer Genomics, as well as numerous biospecimen collections sponsored by funded NCH investigators. Cooperative Human Tissue Network is one of six institutions funded by National Cancer Institutes to access to remnant human tissues for biomedical researchers throughout the United States and Canada. Offers expertise in tissue preparation and preservation to meet the research needs of basic and applied scientists. | Cooperative Human Tissue Network, biospecimen procurement, biospecimen banking, biospecimen processing, biospecimen distribution. | NCI UM1CA239754 | Open | SCR_023260 | 2026-08-29 11:33:34 | 0 | |||||||||
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CBaSE Resource Report Resource Website |
CBaSE (RRID:SCR_027765) | software application, software resource, source code | Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer. | Cancer Genes, SNV, indel, gene-specific probabilistic estimates, strength of negative and positive selection, cancer | NCI U54 CA143874; NIGMS R01 GM078598; NIMH R01 MH101244 |
PMID:29106416 | Free, Available for download, Freely available | https://github.com/weghornlab/CBaSE, http://genetics.bwh.harvard.edu/cbase | SCR_027765 | Cancer Bayesian SElection estimation | 2026-08-29 11:35:13 | 0 | |||||||
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T Cell ExTRECT Resource Report Resource Website 1+ mentions |
T Cell ExTRECT (RRID:SCR_027742) | software resource, software toolkit, source code | Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes. | T-cell, T cell receptor excision circle, WES data, hg19 or hg38 aligned genomes, | NCATS UL1TR000100; NCI P30CA023100; NCI R21CA177519; NCI U01CA196406; NHLBI U54HL108460; NIH Office of the Director DP5OD017937; NLM T15LM011271; NSF |
PMID:34497419 | Free, Available for download, Freely available | SCR_027742 | , T cell exome TREC, T cell exome T cell Receptor Excision Circle | 2026-08-29 11:35:30 | 1 | ||||||||
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CoMUT Resource Report Resource Website 1+ mentions |
CoMUT (RRID:SCR_027745) | software library, software resource, software toolkit, source code | Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots. | genomic DNA, phenotype, visualizing genomic and phenotypic information, comutation plots, | NCI R01 CA227388; NCI R37 CA222574; NCI U01 CA233100; NIGMS T32 GM008313; NSF |
PMID:32502231 | Free, Available for download, Freely available | SCR_027745 | 2026-08-29 11:35:30 | 4 |
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