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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Combined Annotation Dependent Depletion Resource Report Resource Website 500+ mentions |
Combined Annotation Dependent Depletion (RRID:SCR_018393) | CADD | sequence analysis software, web service, software application, data processing software, data analysis software, data access protocol, service resource, software resource | Web tool for predicting deleteriousness of variants throughout human genome. Software tool for scoring deleteriousness of single nucleotide variants as well as insertion and deletions variants in human genome. | Human genome, disease, prediction, injurious variant, single nucleotide variant, insertion variant, deletion variant, deleteriousness scoring | has parent organization: University of Washington; Seattle; USA | NCI R01 CA197139; NHGRI U54 HG006493; Brotman Baty Institute for Precision Medicine ; Berlin Institute of Health ; Howard Hughes Medical Institute ; German Research Foundation ; Charite University Medicine Berlin |
PMID:30371827 PMID:24487276 |
Restricted | SCR_018393 | Combined Annotation Dependent Depletion | 2026-08-03 09:37:02 | 579 | ||||||
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GeoDa Resource Report Resource Website 100+ mentions |
GeoDa (RRID:SCR_018559) | software application, data processing software, data analysis software, software resource, data visualization software | Software program for spatial analysis for non geographic information systems specialists. Includes functionality ranging from simple mapping to exploratory data analysis, visualization of global and local spatial autocorrelation, and spatial regression. | Spatial analysis, data analysis, spatial autocorrelation visualization, spatial regression, mapping | NSF BCS 9978058; NCI R01 CA95949 |
DOI:10.1111/j.0016-7363.2005.00671.x | Free, Freely available | SCR_018559 | 2026-08-03 09:37:00 | 192 | |||||||||
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FairSubset Resource Report Resource Website |
FairSubset (RRID:SCR_019102) | web service, data access protocol, software resource | Web tool to choose representative subsets of data for use with replicates or groups of different sample sizes. Used to retain distribution information at single datum level and may be considered for standardized use in fair publishing practices. | Representative data subsets, different sample sizes groups, different sample sizes replicates, retaining distribution information, fair publishing | NCI CA207729; Polish government grant |
PMID:31583263 | Free, Freely available | SCR_019102 | 2026-08-03 09:37:09 | 0 | |||||||||
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GSVA Resource Report Resource Website 100+ mentions |
GSVA (RRID:SCR_021058) | GSVA | software toolkit, software application, data processing software, data analysis software, software resource | Open source software R package for assaying variation of gene set enrichment over sample population.Used for microarray and RNA-seq data analysis. Gene set enrichment method that estimates variation of pathway activity over sample population in unsupervised manner. | Gene set enrichment, variation estimation, pathway activity, sample population, microarray, RNA-seq, data analysis | is listed by: Bioconductor | ISCIII COMBIOMED ; Spanish MINECO ; NCI U54 CA149237 |
PMID:23323831 | Free, Available for download, Freely available | SCR_021058 | Gene Set Variation Analysis | 2026-08-03 09:37:31 | 256 | ||||||
|
ArchR Resource Report Resource Website 100+ mentions |
ArchR (RRID:SCR_020982) | software toolkit, software application, data processing software, data analysis software, software resource | Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing. | single-cell ATAC-seq data analysis, single-cell ATAC-seq data processing, single cell chromatin accessibility analysis, doublet removal, single cell clustering, cell type identification, unified peak set generation, cellular trajectory identification, transcription factor footprinting | NHGRI RM1 HG007735; NHGRI UM1 HG009442; NCI R35 CA209919; NHGRI UM1 HG009436; NCI U2C CA233311; NIAID U19 AI057266; NIA K99 AG059918; American Society of Hematology Scholar Award ; International Collaborative Award ; Defense Advanced Research Project Agency ; Ray and Dagmar Dolby Family Fund ; Stanford Cancer Institute-Goldman Sachs Foundation Cancer Research Award |
PMID:33633365 | Free, Available for download, Freely available | https://github.com/GreenleafLab/ArchR, https://www.archrproject.com/, https://github.com/GreenleafLab/ArchR_2020 | SCR_020982 | 2026-08-03 09:37:14 | 358 | ||||||||
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MCMICRO Resource Report Resource Website 10+ mentions |
MCMICRO (RRID:SCR_021048) | image processing software, software resource, software application, data processing software | Open source software tool as multiple choice microscopy pipeline for multiplexed whole slide imaging and tissue microarrays. Scalable, modular image processing pipeline for multiplexed tissue imaging. Used for performing sequential steps needed to transform large, multi channel whole slide images into single cell data. | NCI U54 CA225088; Harvard Medical School ; Ludwig Cancer Research Foundation ; University of Zurich BioEntrepreneur Fellowship ; Swiss National Science Foundation Early Postdoc Mobility fellowship |
DOI:10.1101/2021.03.15.435473 | Free, Available for download, Freely available | https://github.com/labsyspharm/mcmicro | SCR_021048 | 2026-08-03 09:37:15 | 11 | |||||||||
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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 | service resource, access service resource, core facility | 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 | 2026-08-03 09:38:26 | 0 | |||||
|
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 | service resource, access service resource, core facility | 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 | 2026-08-03 09:38:12 | 0 | ||||||
|
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 | service resource, access service resource, core facility | 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 | 2026-08-03 09:38:12 | 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 | service resource, access service resource, core facility | 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 | 2026-08-03 09:38:12 | 0 | ||||||
|
MRDetect Resource Report Resource Website |
MRDetect (RRID:SCR_024766) | software resource, data processing software, software application, data analysis software | Software application to estimate presence of MRD in plasma cfDNA WGS through evaluation of matched tumour-derived mutations (SNVs or CNVs). | estimate presence of MRD in plasma cfDNA WGS, evaluation of matched tumour-derived mutations, | NCI DP2 CA239065 | PMID:32483360 | Restricted | SCR_024766 | 2026-08-03 09:38:50 | 0 | |||||||||
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Minerva Resource Report Resource Website |
Minerva (RRID:SCR_024750) | Minerva | software resource, data visualization software, software application, data processing software | Software tools for interactive viewing and fast sharing of large image data. Comprises Minerva Author, a tool to create and annotate images, and Minerva Story, a narrative image viewer for web hosting. Used for interpreting and interacting with complex images, organized around guided analysis approach. Enables fast sharing of large image data that is stored on Amazon S3 and viewed using zoomable image viewer implemented using OpenSeadragon, making it ideal for integration into multi-omic browsers for data dissemination of tissue atlases. | tissue atlases, digital pathology, interactive viewing and sharing of large image data, data dissemination of tissue atlases, | has parent organization: Harvard University; Cambridge; United States | Gates ; NCI U54CA225088; NCI U2CCA233262; NCI U2C CA233280; Ludwig Cancer Center at Harvard ; NCI P30 CA06516 |
PMID:33768192 | Free, Freely available | https://www.cycif.org/software/minerva, https://github.com/labsyspharm/minerva-story | SCR_024750 | Minerva Author, Minerva Story | 2026-08-03 09:38:24 | 0 | |||||
|
scimap Resource Report Resource Website 10+ mentions |
scimap (RRID:SCR_024751) | software toolkit, software application, data processing software, data analysis software, software resource, data visualization software | Software toolkit for analyzing spatial molecular data. Underlying framework is generalizable to spatial datasets mapped to XY coordinates. Package uses anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. Python based implementation efficiently deals with large datasets of millions of cells. | Python, spatial single cell analysis, spatial datasets, analyzing spatial molecular data, | has parent organization: Harvard University; Cambridge; United States | NCI K99 CA256497 | Free, Available for download, Freely available | https://github.com/labsyspharm/scimap | SCR_024751 | 2026-08-03 09:38:21 | 10 | ||||||||
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CRAPome Resource Report Resource Website 10+ mentions |
CRAPome (RRID:SCR_025008) | web service, database, data access protocol, data or information resource, software resource | 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, | NIGMS 5R01GM94231; NIDA DP1DA026192; NHLBI HL112618-01; Canadian Institutes of Health Research ; government of Ontario ; Austrian Academy of Sciences ; Austrian Federal Ministry for Science and Research ; European Research Council ; Austrian Science Fund ; European Molecular Biology Organisation ; Netherlands Proteomics Center ; European Union 7th Framework Program ; Stowers Institute for Medical Research ; Human Frontier Science Program ; NCI R21 CA16006001A1 |
PMID:23921808 | Free, Freely available, | https://reprint-apms.org/ | SCR_025008 | CRAPome:Contaminant Repository for Affinity Purification | 2026-08-03 09:38:31 | 16 | |||||||
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ReDU Resource Report Resource Website 1+ mentions |
ReDU (RRID:SCR_025105) | web service, data access protocol, software resource | 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 | NIGMS P41 GM103484; NCI R03 CA211211; NIGMS R01 GM107550; Sloan Foundation ; Gordon and Betty Moore Foundation ; American Society for Mass Spectrometry ; NSF ; Netherlands eScience Center ; FAPESP ; Krupp Endowed Fund ; US Office of Naval Research ; University of California ; San Diego Center for Microbiome Innovation SEED grants |
PMID:32807955 | Free, Freely available | SCR_025105 | Reanalysis of Data User | 2026-08-03 09:38:25 | 1 | |||||||
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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 | service resource, access service resource, core facility | 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 | 2026-08-03 09:37:48 | 1 | |||||
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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) | service resource, access service resource, core facility | 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 | 2026-08-03 09:37:54 | 51 | ||||||
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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 | service resource, access service resource, core facility | 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 | 2026-08-03 09:37:58 | 17 | ||||||
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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) | service resource, access service resource, core facility | 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 |
NIH Office of the Director S10 OD026929; NIDDK P30DK063491; NCI P30CA023100; NIDDK P30DK120515 |
ABRF_1025 | https://coremarketplace.org/?FacilityID=1025&citation=1 | SCR_022740 | UCSD IGM Genomics Center | 2026-08-03 09:37:47 | 1 | |||||||
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IPD - Immuno Polymorphism Database Resource Report Resource Website 10+ mentions |
IPD - Immuno Polymorphism Database (RRID:SCR_003004) | IPD | data or information resource, database | A set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: * IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, * IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; * IPD-human platelet antigens, alloantigens expressed only on platelets and * IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterized melanoma cell lines. | polymorphic gene, immune system, gene, gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
European Union contract QLRI-CT-200!-01325; NCI P01 111412 |
PMID:19875415 PMID:18449992 PMID:15608253 |
biotools:ipd, nif-0000-03038, r3d100010797 | https://bio.tools/ipd, https://doi.org/10.17616/R3KK7K | SCR_003004 | IPD-The Immuno Polymorphism Database, IPD - The Immuno Polymorphism Database | 2026-08-03 09:32:10 | 24 |
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