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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | data analytics software, software application, software resource | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
B&J Cardan Oncology Research Fund ; Damon Runyon Cancer Research Foundation ; Doris Duke Charitable Foundation ; Ludwig Institute for Cancer Research ; NCI T32 CA09302; NCI U01 CA154969; NIAID U19 AI090019; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation ; US Department of Defense |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | SciCrunch Registry | 2026-10-24 12:51:48 | 1908 | ||||||
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Differential Gene Correlation Analysis Resource Report Resource Website 1+ mentions |
Differential Gene Correlation Analysis (RRID:SCR_020964) | DGCA | data analysis software, data processing software, software application, software resource | Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix. | Differential gene, gene, gene correlation, correlation analysis, input matrices, differential correlations, identifier pairs, gene expression data, calculate differential correlations | is listed by: CRAN | NCI R01 CA163772; NIAID U01 AI111598; NIA F30 AG052261; NIA R01 AG046170 |
PMID:27846853 | Free, Available for download, Freely available | https://github.com/andymckenzie/DGCA | SCR_020964 | SciCrunch Registry | 2026-10-24 12:49:16 | 1 | ||||||
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Markov Affinity based Graph Imputation of Cells Resource Report Resource Website 50+ mentions |
Markov Affinity based Graph Imputation of Cells (RRID:SCR_022371) | MAGIC | data analysis software, data processing software, software application, software resource | Software tool for imputing missing values restoring structure of large biological datasets.Method that shares information across similar cells, via data diffusion, to denoise cell count matrix and fill in missing transcripts. | imputing missing values, restoring structure, shares information across similar cells, denoise cell count matrix, fill in missing transcripts | American Cancer Society ; NCI P30 CA008748; NCI R01 CA164729; NICHD DP1 HD084071; Simons SFARI grants |
PMID:29961576 | Free, Available for download, Freely available | SCR_022371 | SciCrunch Registry | 2026-10-24 12:49:19 | 86 | ||||||||
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miQC Resource Report Resource Website 1+ mentions |
miQC (RRID:SCR_022697) | data analysis software, data processing software, software application, software resource | Software tool as flexible, probablistic metrics for quality control of scRNA-seq data. Adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. Data driven QC metric that jointly models proportion of reads mapping to mtDNA and number of detected genes with mixture models in probabilistic framework to predict which cells are low quality in given dataset. | scRNA-seq data quality control, QC metric, low quality data prediction, single cell RNA-sequencing data | Academy of Finland ; Cancer Foundation Finland ; European Union Horizon 2020 research and innovation program ; NCI CA237170; NHGRI HG009007 |
PMID:34428202 | Free, Available for download, Freely available | SCR_022697 | SciCrunch Registry | 2026-10-24 12:49:21 | 4 | |||||||||
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Minimum Information about Tissue Imaging Resource Report Resource Website |
Minimum Information about Tissue Imaging (RRID:SCR_022830) | MITI | consortium, data or information resource, narrative resource, organization portal, portal, standard specification | Consortium provides guidelines for highly multiplexed tissue images. Standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology. Data and metadata standards consistent with Findable, Accessible, Interoperable, and Reusable (FAIR) standards that guide data deposition, curation and release. | Data and metadata standards, FAIR, tissue imaging, minimum information standard, guidelines for highly multiplexed tissue images | NCI U2C CA233195; NCI U2C CA233238; NCI U2C CA233254; NCI U2C CA233262; NCI U2C CA233280; NCI U2C CA233284; NCI U2C CA233285; NCI U2C CA233291; NCI U2C CA233303; NCI U2C CA233311; NCI U54 CA225088 |
PMID:35277708 | Free, Freely available | https://github.com/miti-consortium/MITI | SCR_022830 | SciCrunch Registry | MITI Consortium | 2026-10-24 12:49:22 | 0 | ||||||
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caHUB Resource Report Resource Website |
caHUB (RRID:SCR_009657) | caHUB | data or information resource, narrative resource, standard specification | THIS RESOURCE IS NO LONGER IN SERVICE. Documented July 5, 2018. A national center for biospecimen science and standards to advance cancer research and treatment. It was created in response to the critical and growing need for high-quality, well-documented biospecimens for cancer research. The initiative builds on resources already developed by the NCI, including the Biospecimen Research Network and the NCI Best Practices for Biospecimen Resources, both of which were developed to address challenges around standardization of the collection and dissemination of quality biospecimens. caHUB will develop the infrastructure for collaborative biospecimen research and the production of evidence-based biospecimen standard operating procedures. | biospecimen, clinical, biomaterial supply resource, tissue |
is listed by: NIDDK Information Network (dkNET) is related to: Biorepositories and Biospecimens Research Branch has parent organization: National Cancer Institute |
Cancer | NCI ; ARRA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156094 | SCR_009657 | SciCrunch Registry | The Cancer Human Biobank, cancer Human Biobank | 2026-10-24 12:49:24 | 0 | |||||
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ChIP-X Enrichment Analysis 3 Resource Report Resource Website 100+ mentions |
ChIP-X Enrichment Analysis 3 (RRID:SCR_023159) | ChEA3 | software resource, web application | Web based transcription factor enrichment analysis. Web server ranks TFs associated with user-submitted gene sets. ChEA3 background database contains collection of gene set libraries generated from multiple sources including TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, and TF-gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate composite rank that improves prediction of correct upstream TF compared to ranks produced by individual libraries. | Transcription Factor, gene sets, transcription factor enrichment analysis, TF-gene co-expression from RNA-seq studies, TF-target associations from ChIP-seq experiments, TF-gene co-occurrence, prediction of correct upstream, | NCI U24CA224260; NHLBI U54HL127624; NIGMS T32GM062754; NIH Office of the Director OT3OD025467 |
PMID:31114921 | Free, Freely available | SCR_023159 | SciCrunch Registry | ChIP-X Enrichment Analysis Version 3 (ChEA3) | 2026-10-24 12:49:28 | 193 | |||||||
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SPRING Resource Report Resource Website 10+ mentions |
SPRING (RRID:SCR_023578) | data access protocol, software resource, web service | Interactive web tool to visualize single cell data using force directed graph layouts. Kinetic interface for visualizing high dimensional single cell expression data. Collection of pre-processing scripts and web browser based tool for visualizing and interacting with high dimensional data. | visualizing high dimensional single cell expression data, single cell expression data visualization, high dimensional data, | has parent organization: Harvard University; Cambridge; United States | Burroughs-Wellcome Career Award at the Scientific Interface ; Edward J Mallinckrodt Foundation Fellowship ; NCI 1R33CA212697; NIGMS 5T32GM080177 |
PMID:29228172 | Free, Available for download, Freely available | https://github.com/AllonKleinLab/SPRING/, https://github.com/AllonKleinLab/SPRING_dev | SCR_023578 | SciCrunch Registry | 2026-10-24 12:49:32 | 26 | |||||||
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HemOnc Knowledgebase Resource Report Resource Website 1+ mentions |
HemOnc Knowledgebase (RRID:SCR_023436) | data or information resource, disease-related portal, portal, topical portal | Medical wiki of interventions, regimens, and general information relevant to fields of hematology and oncology. Knowledge base for hematology and oncology providers, containing details about hematology/oncology drugs and treatment regimens. Any healthcare professional can sign up to contribute. Acuracy and completeness of content is overseen by Editorial Board. | Hematology and oncology knowledge base, hematology providers, oncology providers, hematology reference, oncology reference, hematology, oncology, drug interventions, treatment regimens, reference, healthcare professional, | cancer | NCI U24 CA265879 | Free, Freely available | https://hemonc.org/wiki/ | SCR_023436 | SciCrunch Registry | , HemOnc, Free Hematology/Oncology Reference, HemOnc.org | 2026-10-24 12:49:31 | 7 | |||||||
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AccuCor Resource Report Resource Website 10+ mentions |
AccuCor (RRID:SCR_023046) | data processing software, software application, software resource | Software as isotope natural abundance correction algorithm that is needed especially for high resolution mass spectrometers. Natural abundance correction of mass spectrometer data. | Natural abundance correction, mass spectrometer data, isotope natural abundance correction algorithm, high resolution mass spectrometers | NCI CA211437; NCI R01 CA163591; NIDDK P30DK019525; U. S. Department of Energy |
PMID:28471646 | Free, Available for download, Freely available | https://github.com/XiaoyangSu/AccuCor | SCR_023046 | SciCrunch Registry | 2026-10-24 12:50:08 | 27 | ||||||||
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UCSF Brain Tumor Tissue Bank Resource Report Resource Website |
UCSF Brain Tumor Tissue Bank (RRID:SCR_000647) | biomaterial supply resource, material resource, tissue bank | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Brain Tumor Research Center Tissue Bank began collecting tissue in 1978 and has established an organized repository of characterized tissues--frozen, paraffin-embedded, blood and cultures--that are maintained in a manner useful for a wide range of studies. Samples are collected only from patients who have agreed to have their tissues banked and used for future research. Consent documents are maintained in a secure area and associated clinical data are held in a double-password protected computer database. Each sample received into the Tissue Bank is non-identifying number. No protected health information (PHI) is released. To obtain samples, investigators submit a request form to the Manager. The request form requires an explanation of the tissue requested (type, number of samples, justification), description of the study, CHR approval (see new policy regarding human vs. non-human research) and Project Leader authorization. The Manager reviews each request for feasibility before presentation to the Scientific Core Committee. The UCSF Neurosurgery Tissue Bank makes its inventory of stock cell lines available to all investigators. Requested cells are grown in T-25 flasks and shipped FedEx Priority Overnight at the receipient's expense. However, if you prefer, we can ship the frozen cells, packed in dry ice. (Note: some countries restrict dry ice shipments.) | tissue, frozen, paraffin-embedded, blood, culture, frozen tissuefrozen serum, serum, paraffin embedded tissue, research, cell, cell line |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of California at San Francisco; California; USA |
Tumor | NINDS P01 NS94297; NCI P-50-CA97257 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_33528, SCR_006439, nlx_143683 | https://gnome.ucsf.edu/tbank/ | SCR_000647 | SciCrunch Registry | UCSF Brain Tumor Research Center Tissue Bank, UCSF Brain Tumor Research Center Tissue Core, UCSF Neurosurgery Tissue Bank, UCSF Neurological Surgery Tissue Bank, UCSF BTRC Tissue Core | 2026-10-24 12:50:18 | 0 | |||||
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Biospecimen Research Database Resource Report Resource Website 1+ mentions |
Biospecimen Research Database (RRID:SCR_001944) | data or information resource, database | Database to find literature, established protocols, and best practices for collecting, storing, and handling biological samples. Its main purpose is to help researchers improve the quality and reproducibility of biospecimen-based medical and genetic research. Provides a library of validated protocols that laboratories use to properly process human biospecimens (like blood or tissue) without degrading their molecular integrity. Offers procedural guidelines (BEBPs) backed by scientific literature to protect samples from pre-analytical variables (e.g., storage temperature, time-to-freezing). Catalogs thousands of peer-reviewed articles focused on biospecimen science. | NCI, biospecimen, biomarker, gene, standard operating procedure, sop, database |
is related to: Biorepositories and Biospecimens Research Branch has parent organization: National Cancer Institute has parent organization: National Institutes of Health |
NCI | PMID:25757745 | Free, Freely available | SciRes_000169 | https://dctd.cancer.gov/programs/cdp/organization/bbrb | https://brd.nci.nih.gov/brd/ | SCR_001944 | SciCrunch Registry | NCI Biospecimen Research Database, Biospecimen Research Database (BRD) | 2026-10-24 12:50:21 | 5 | ||||
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University of Pennsylvania Genomics Analysis Core Resource Report Resource Website |
University of Pennsylvania Genomics Analysis Core (RRID:SCR_011061) | UPenn DNA Sequencing Facility, Penn DNA Sequencing Facility | access service resource, core facility, service resource | Core facility that provides the following services: Large sequencing project support, Sanger sequencing service, High throughput DNA sequencing, Ion Torrent Personal Genome Machine sequencing, Template preparation and purification, Roche 454 sequencing, Sequence analysis and database search support, Construction of targeting vector for gene targeting, Genotyping and Fragment Analysis service, Molecular biology services, Mouse genotyping, and Ion Personal Genome Machine sequencing data analysis. The DNA Sequencing Facility provides long read, automated Sanger sequencing; microsatellite-based genotyping and fragment analysis; plasmid and BAC DNA preparation and purification; and related molecular biological services including PCR, cloning, sub-cloning, site-directed mutagenesis, and preparation of targeting vectors for gene targeting in mice. Core also provides services and support for analysis and interpretation of sequence data as well as the design of approaches to complex sequencing projects. For the last four years the facility has been providing Roche 454 sequencing service that includes library preparation, emulsion PCR and pyrosequencing for both genomic DNA and amplicons. | dna sequencing, chain termination sequencing, next generation sequencing, plasmid purification, dna purification, metagenomics analysis, pyrosequencing, rna sequencing, bioinformatics analysis, knockout mouse generation, construct engineering, microsatellite analysis, single-nucleotide polymorphism analysis, genotyping assay, site-directed mutagenesis, polymerase chain reaction, recombinant plasmid cloning, transgenic mouse model generation |
is listed by: ScienceExchange is listed by: Eagle I has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
NCI P30 CA016520 | Available to external user | SciEx_9913 | SCR_011061 | SciCrunch Registry | , University of Pennsylvania, Perelman School of Medicine, Penn, DNA Sequencing Facility, UPenn | 2026-10-24 12:52:27 | 0 | ||||||
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Texas University Health Science Center at San Antonio Long School of Medicine Department of Cell Systems and Anatomy Optical Imaging Core Facility Resource Report Resource Website 1+ mentions |
Texas University Health Science Center at San Antonio Long School of Medicine Department of Cell Systems and Anatomy Optical Imaging Core Facility (RRID:SCR_012171) | UTHSCSA OIF | access service resource, core facility, service resource | Service resource which makes imaging technology available to investigators on UTHSCSA campus and neighboring scientific community. Core Optical Imaging Facility offers access to technology for imaging of living cells, tissues, and animals, consultation, education and assistance regarding theory and application of optical imaging techniques, technical advice on specimen preparation techniques and probe selection. | Optical, imaging, facility, living, cell, tissue, animal, consultation, speciment, preparation |
is listed by: ScienceExchange has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA |
NCI ; NIA P01 AG19316; UTHSCSA |
Restricted | SciEx_10134 | http://www.scienceexchange.com/facilities/optical-imaging-facility-oif | SCR_012171 | SciCrunch Registry | University of Texas Health Science Center at San Antonio Optical Imaging Facility, University of Texas Health Science Center at San Antonio Optical Imaging Facility (OIF), UTHSCSA Optical Imaging Facility, UTHSCSA Optical Imaging Facility (OIF) | 2026-10-24 12:52:35 | 1 | |||||
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Moffitt Cancer Center Tissue Core Facility Resource Report Resource Website 1+ mentions |
Moffitt Cancer Center Tissue Core Facility (RRID:SCR_012364) | Moffitt Tissue Core | access service resource, core facility, service resource | Biorepository resource with mission of proper collection, handling, processing and storage of irreplaceable biological specimens to support spectrum of related basic science, translational and clinical research. Provides expertise in nucleic acid extractions, quantification, aliquoting and quality assurance; liquid specimen centrifugation, processing and aliquoting; histological tissue processing, immunohistochemistry and tissue microarray microtomy; pathologist consultation services. Tissue Core operations are divided into four distinct pillars of service that work collaboratively to ensure specimen quality is maintained from procurement to preservation. |
is listed by: ScienceExchange is listed by: ABRF CoreMarketplace has parent organization: Moffitt Cancer Center |
NCI P30 CA076292 | ABRF_2739, SciEx_12211 | https://coremarketplace.org/?FacilityID=2739&citation=1 | http://www.scienceexchange.com/facilities/tissue-core-facility-moffitt | SCR_012364 | SciCrunch Registry | , H. Lee Moffitt Cancer Center and Research Institute Tissue Core Facility | 2026-10-24 12:52:36 | 2 | ||||||
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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 | SciCrunch Registry | Antibody and Bioresource Core Facility | 2026-10-24 12:52:54 | 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 | SciCrunch Registry | Vincent Coates Foundation Mass Spectrometry Laboratory | 2026-10-24 12:52:57 | 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 | SciCrunch Registry | Robert H. Lurie Comprehensive Cancer Center Flow Cytometry Core Facility | 2026-10-24 12:52:55 | 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 | SciCrunch Registry | Pathology Core Facility | 2026-10-24 12:52:56 | 3 | ||||||||
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North Carolina University at Chapel Hill R.L. Juliano Structural Bioinformatics Core Facility Resource Report Resource Website |
North Carolina University at Chapel Hill R.L. Juliano Structural Bioinformatics Core Facility (RRID:SCR_017836) | access service resource, core facility, service resource | Core provides consultations and collaborations on research studies requiring computational structural biology methods. Analyses available are to study of static structures, molecular dynamics studies for analyzing contribution of dynamic and collective motions to macromolecular functionality. Trains researchers in computational structural biology techniques, or works in collaborative manner with researchers.Provides access to software tools for protein and DNA sequence analysis, protein fold determination, homology modeling, active site identification, and analysis of effects of various mutations on structure and function of protein, along with additional computational analyses. | Computational, structural, biology, method, analysis, training, service, core, ABRF | is listed by: ABRF CoreMarketplace | NCI P30 CA016086 | Open | ABRF_628 | SCR_017836 | SciCrunch Registry | R. L. Juliano Structural Bioinformatics Core facility at UNC-Chapel Hill | 2026-10-24 12:52:57 | 0 |
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