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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Annotare Resource Report Resource Website |
Annotare (RRID:SCR_000319) | software resource, software application, standalone software | A software tool for annotating biomedical investigations and the resulting data, then producing a MAGE-TAB file. This software is a standalone desktop which features: an editor function, an annotation modifier, incorporation of terms from biomedical ontologies, standard templates for common experiment types, a design aid to help create a new document, and a validator that checks for syntactic and semantic violations. | biomedical research, magetab, editor, annotation, biomedical ontology | is listed by: OMICtools | NIBIB ; NCI ; NHGRI P41 HG003619 |
PMID:20733062 | Free, Available for download, Freely available | OMICS_00741 | SCR_000319 | annotare: a tool for annotating high-throughput biomedical investigations and resulting data | 2026-08-03 09:31:01 | 0 | ||||||
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nondetects Resource Report Resource Website 1+ mentions |
nondetects (RRID:SCR_001702) | software resource, software application, standalone software | Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data. | mac os x, unix/linux, windows, r, assay domain, gene expression, preprocessing, technology, workflow step, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
NCI CA009363; NCI CA138249; NHGRI HG006853; Edelman-Gardner Foundation |
PMID:24764462 | Free, Available for download, Freely available | OMICS_03938, biotools:nondetects | https://bio.tools/nondetects | SCR_001702 | nondetects - Non-detects in qPCR data | 2026-08-03 09:31:28 | 1 | |||||
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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 | service resource, access service resource, core facility | 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 | 2026-08-03 09:37:58 | 0 | |||||||||
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University of California Davis Health Biostatistics Shared Resource Core Facility Resource Report Resource Website |
University of California Davis Health Biostatistics Shared Resource Core Facility (RRID:SCR_023585) | BSR | service resource, access service resource, core facility | Provides expertise in design, analysis and reporting of cancer related studies, including basic, translational, clinical and population based research. BSR affiliated faculty and staff work with investigators from the earliest stages of study planning. The shared resource is especially committed to mentoring early career cancer researchers. | USEDit, ABRF, cancer related studies, biostatistics |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of California at Davis; California; USA |
NCI P30CA093373 | ABRF_1766 | https://coremarketplace.org/?FacilityID=1766&citation=1 | SCR_023585 | University of California, Davis UC Davis Biostatistics Shared Resource, UC Davis Biostatistics Shared Resource | 2026-08-03 09:38:05 | 0 | ||||||
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University of California Davis Health Combinatorial Chemistry and Chemical Biology Shared Resource Core Facility Resource Report Resource Website |
University of California Davis Health Combinatorial Chemistry and Chemical Biology Shared Resource Core Facility (RRID:SCR_023584) | CCCBSR | service resource, access service resource, core facility | Provides high throughput screening platform to discover unique chemical probes against biological targets using various one bead one compound and one bead two compound combinatorial libraries.Interacts closely with resource users on optimization of the lead compounds via focused libraries and standard medicinal chemistry techniques. Provides custom synthesis of telodendrimer based micellar nanoparticle platform for efficient drug delivery. | USEDit, ABRF, high throughput screening, discover unique chemical probes against biological targets, custom synthesis of telodendrimer based micellar nanoparticle, drug delivery, |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of California at Davis; California; USA |
NCI P30CA093373 | ABRF_1767 | https://coremarketplace.org/?FacilityID=1767&citation=1 | SCR_023584 | Davis UC Davis Combinatorial Chemistry & Chemical Biology Shared Resource, UC Davis Combinatorial Chemistry & Chemical Biology Shared Resource, University of California | 2026-08-03 09:38:26 | 0 | ||||||
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University of California Davis Health Molecular Pharmacology Shared Resource Core Facility Resource Report Resource Website |
University of California Davis Health Molecular Pharmacology Shared Resource Core Facility (RRID:SCR_023588) | MPSR | service resource, access service resource, core facility | Provides services to support the development and implementation of clinical trials at UC Davis Comprehensive Cancer Center. Oversees high quality collection, processing, and analysis of clinical specimens,typically but not exclusively blood specimens, for pharmacokinetic and pharmacodynamics studies. Conducts preclinical modeling of novel anti cancer agents to test hypotheses and develop scientific rationale required for translation of laboratory concepts into clinical trials, including assessment of DM/PK/PD properties. | USEDit, ABRF, development and implementation of clinical trials, clinical specimens, blood specimens, preclinical modeling of novel anti cancer agents, |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: University of California at Davis; California; USA |
NCI P30CA093373 | Restricted | ABRF_1771 | https://coremarketplace.org/?FacilityID=1771&citation=1 | SCR_023588 | UC Davis Molecular Pharmacology Shared Resource, Davis UC Davis Molecular Pharmacology Shared Resource, University of California | 2026-08-03 09:38:05 | 0 | |||||
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Stanford University School of Medicine Cancer Institute Biostatistics Shared Resource Core Facility Resource Report Resource Website 1+ mentions |
Stanford University School of Medicine Cancer Institute Biostatistics Shared Resource Core Facility (RRID:SCR_023696) | BSR | service resource, access service resource, core facility | Core provides statistical support to SCI members by engages them on their data related needs. Specifically, BSR members assist researchers at each stage of study’s lifecycle, including project design, mid study evaluation and interpretation and reporting of results. In addition, BSR members mentor SCI investigators in research methods. BSR assists with development and review of proposed studies and planning of research related data management systems. | ABRF, USEDit, statistical support, project design, mid study evaluation and interpretation, results reporting, |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Stanford University; Stanford; California |
NCI | Restricted | ABRF_2509 | https://coremarketplace.org/?FacilityID=2509&citation=1, https://coremarketplace.org/RRID:SCR_023696?citation=1 | SCR_023696 | , Stanford Cancer Institute Biostatistics Shared Resource, Stanford Biostatistics Shared Resource | 2026-08-03 09:38:13 | 1 | |||||
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Drugmonizome Resource Report Resource Website 1+ mentions |
Drugmonizome (RRID:SCR_024821) | data or information resource, database | Database with search engine for querying annotated sets of drugs and small molecules for performing drug set enrichment analysis. | annotated sets of drugs and small molecules, searching of annotated sets of drugs and small molecules, drugs, small molecules, | NCI U24CA224260; NHLBI U54HL127624; NIH Office of the Director OT2OD030160 |
PMID:33787872 | Free, Freely available | SCR_024821 | 2026-08-03 09:38:26 | 1 | |||||||||
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Natural Products Atlas Resource Report Resource Website 10+ mentions |
Natural Products Atlas (RRID:SCR_025107) | NP Atlas | data or information resource, atlas, knowledge base | Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles. | FAIR principles, microbial natural products discovery, natural product structures, bacterial and fungal natural products, visualize chemical diversity, | has parent organization: Simon Fraser University; British Columbia; Canada | NSERC Discovery ; NCCIH U41 AT008718; NIGMS R01 GM125943; NCCIH F31 AT010098; NCI F31 CA236237; NCCIH T32 AT007533; NIH D43 TW010530; NSF ; BBSRC ; Carnegie Trust for the Universities of Scotland ; Netherlands eScience Center ; Sao Paulo Research Foundation ; NCCIH AT008718; NIGMS GM124461; Natural Sciences and Engineering Research Council of Canada ; Ministry of Science ; Technology and Telecommunications of Costa Rica |
PMID:31807684 DOI:10.1093/nar/gkab941 |
Free, Freely available, | SCR_025107 | , The Natural Products Atlas, The Natural Products Atlas 2.0 | 2026-08-03 09:38:33 | 19 | ||||||
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PhysiCell Studio Resource Report Resource Website 10+ mentions |
PhysiCell Studio (RRID:SCR_025311) | software resource, source code | Software graphical tool to allow easy editing of (XML) model, create initial positions of cells, run simulation, and visualize results. To contribute, fork and make PRs to the development branch. Used to create, execute, and visualize multicellular model using PhysiCell. | create, execute, visualize, multicellular model, create initial positions of cells, | NSF ; NCI U01 CA232137; Breast Cancer Research Foundation ; Jayne Koskinas Ted Giovanis Foundation for Health and Policy ; European Commission |
PMID:37961612 | Free, Available for download, Freely available | SCR_025311 | 2026-08-03 09:38:42 | 15 | |||||||||
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MatrixEQTL Resource Report Resource Website 50+ mentions |
MatrixEQTL (RRID:SCR_025513) | software resource, data processing software, software application, data analysis software | Software tool for ultra fast eQTL analysis via large matrix operations. | expression Quantitative Trait Loci, fast eQTL analysis, large matrix operations, | NIMH R01 MH090936; NIEHS R01 ES015241; US Environmental Protection Agency ; NCI R01 CA138255; NSF ; Gillings Innovation Laboratory in Statistical Genomics |
PMID:22492648 | Free, Freely available, | SCR_025513 | Matrix Expression Quantitative Trait Loci | 2026-08-03 09:39:10 | 69 | ||||||||
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scGBM Resource Report Resource Website 1+ mentions |
scGBM (RRID:SCR_025518) | software resource, source code | Software application for model-based dimensionality reduction of scRNA-seq data. Quantifies uncertainty in each cell's latent position and leverages these uncertainties to assess confidence associated with given cell clustering. On real and simulated single-cell data produces low-dimensional embeddings that better capture relevant biological information while removing unwanted variation. Used for model-based dimensionality reduction for single-cell RNA-seq with generalized bilinear models. | Generalized bilinear models, model-based dimensionality reduction, scRNA-seq data, removing unwanted variation, | NCI T32CA009337; NCI R01CA240299 |
PMID:37162914 | Free, Available for download, Freely available, | SCR_025518 | 2026-08-03 09:38:48 | 2 | |||||||||
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MRQy Resource Report Resource Website 1+ mentions |
MRQy (RRID:SCR_025779) | software resource, data processing software, software application, data analysis software | 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 U24CA199374; NCI R01CA202752; NCI R01CA208236; NCI R01CA216579; NCI R01CA220581; NCI 1U01CA239055; NCI 1F31CA216935; NCI 1U01CA248226; NHLBI R01HL15127701A1; NIBIB 1R43EB028736; NCRR 1C06RR12463 |
PMID:33176026 | Free, Available for download, Freely available | SCR_025779 | 2026-08-03 09:38:51 | 1 | |||||||||
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Moffitt spatialGE Resource Report Resource Website 1+ mentions |
Moffitt spatialGE (RRID:SCR_025980) | software resource, web application | Web application, a user friendly, point-and-click implementation of spatialGE R package. Contains collection of methods for visualization and spatial statistics analysis of tissue microenvironment and heterogeneity using spatial transcriptomics experiments. Used for user-friendly analysis of spatial transcriptomics data. | Moffitt Cancer Center, spatial transcriptomics data analysis, implementation of spatialGE R package, methods for visualization and spatial statistics analysis, tissue microenvironment and heterogeneity, spatial transcriptomics experiments, | NCI U01 CA274489; NCI T32 CA23339 |
DOI:10.1101/2024.06.27.601050 | Free, Freely available | SCR_025980 | Moffitt Cancer Center spatialGE, spatialGE | 2026-08-03 09:38:39 | 1 | ||||||||
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STAR-Fusion Resource Report Resource Website 10+ mentions |
STAR-Fusion (RRID:SCR_025853) | software resource, source code | Software tool to leverage chimeric and discordant read alignments identified by STAR aligner to predict fusions. Component of Trinity Cancer Transcriptome Analysis Toolkit. Used to identify candidate fusion transcripts supported by Illumina reads. Maps junction reads and spanning reads to reference annotation set. | identify candidate fusion transcripts, predict fusions, leverages chimeric and discordant read alignments, chimeric, discordant, read alignment, | Howard Hughes Medical Institute ; Klarman Cell Observatory ; NCI U24CA180922; NCI R50CA211461; NCI R21CA209940; NCI U01CA214846 |
PMID:31639029 | Free, Available for download, Freely available | SCR_025853 | 2026-08-03 09:38:51 | 33 | |||||||||
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scVital Resource Report Resource Website |
scVital (RRID:SCR_026215) | software resource, software application, source code | Software tool to embed scRNA-seq data into species-agnostic latent space to overcome batch effect and identify cell states shared between species. Deep learning algorithm for cross-species integration of scRNA-seq data. | embed scRNA-seq data, species-agnostic latent space, overcome batch effect, identify cell states shared between species, cross-species integration, scRNA-seq data, | NIA R01 AG054720; NCI K08 CA267072; NCI R01 CA290400; NCI P30 CA08748 |
DOI:10.1101/2024.12.20.629285 | Free, Available for download, Freely available | SCR_026215 | 2026-08-03 09:39:14 | 0 | |||||||||
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DSigDB Resource Report Resource Website 50+ mentions |
DSigDB (RRID:SCR_026202) | data or information resource, database | Online database provides collection of gene sets based on quantitative inhibition and/or drug-induced gene expression changes data of drugs and compounds. Allows users to search, view and download drugs/compounds and gene sets. | gene sets, quantitative inhibition, drug induced, gene expression changes, data, drugs, compounds, | NCI P30CA046934; NCI P50CA058187 |
PMID:25990557 | Free, Freely available, | SCR_026202 | , Drug Signatures Database, drug SIGnatures DataBase | 2026-08-03 09:39:14 | 82 | ||||||||
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TRUST4 Resource Report Resource Website 1+ mentions |
TRUST4 (RRID:SCR_026162) | sequence analysis software, software application, data processing software, source code, data analysis software, software resource | Software tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from fluid and solid tissues, including tumors. Performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 and reports consensus contigs of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to identify the corresponding gene and CDR3 details. TRUST4 supports both single-end and paired-end bulk or single-cell sequencing data with any read length. | analyze TCR and BCR sequences, de novo assembly, unselected RNA sequencing data, fluid and solid tissues, tumors, | NCI U01CA226196; NCI U24CA224316 |
PMID:33986545 | Free, Available for download, Freely available | SCR_026162 | 2026-08-03 09:38:53 | 4 | |||||||||
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TNBCtype Resource Report Resource Website |
TNBCtype (RRID:SCR_026238) | software resource, web application | Website for predicting the subtype of triple negative breast cancer sample based on its gene expression profile. | predicting subtype, triple negative breast cancer sample, gene expression profile, | NCI CA068485; NCI CA95131; NCI CA148375; NCI CA105436; NCI CA070856; NCI CA009385; American Cancer Society ; Komen Foundation |
PMID:22872785 | Free, Freely available | SCR_026238 | 2026-08-03 09:39:15 | 0 | |||||||||
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FACETS Resource Report Resource Website 10+ mentions |
FACETS (RRID:SCR_026264) | software application, data processing software, source code, data analysis software, software resource | Software tool for estimating genome copy numbers from high throughput DNA sequencing data. Allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Used to implement Fraction and Copy number Estimate from Tumor/normal Sequencing. | Allele-specific copy number, clonal heterogeneity analysis, estimating genome copy numbers, high throughput DNA sequencing data, Fraction and Copy number Estimate from Tumor/normal Sequencing, | NCI CA124514; NCI CA163251; NCI CA195365; NCI P01 CA129243; Susan G. Komen for the Cure ; NCI P30 CA008748 |
PMID:27270079 | Free, Available for download, Freely available, | SCR_026264 | 2026-08-03 09:38:45 | 12 |
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