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Multi-data type platforms
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Imaging platforms
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Omics platforms
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Clinical platforms
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All platforms
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Data Resources
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<div id="header">
<h1 class="title toc-ignore"><strong>Data Resources Platforms</strong></h1>
</div>
<div id="overview" class="section level3">
<h3><strong>Overview</strong></h3>
<p>The following table contains a list of cancer data resources that are available to researchers. These resources include genomic, epigenomic, transcriptomic, proteomic, and cancer imaging data.</p>
<strong>Table keys:</strong>
<div title="Table keys">
<p><img src="ITCRLogo.png" height="25"> </img> = ITCR Funded</p>
</div>
<div id="htmlwidget-77089a2f49e7a2385255" style="width:100%;height:auto;" class="datatables html-widget"></div>
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100%;\"/>\n <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n <\/div>\n <\/td>\n<\/tr>","data":[["<b><a href=\"https://www.pdxfinder.org/\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>Patient-Derived Xenograft (PDX) Finder<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://dataverse.harvard.edu/dataverse/HemOnc\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>HemOnc Ontology<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://bioinformatics.mdanderson.org/public-software/ngchm/\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>Next Generation Clustered Heat Maps<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://www.oncomx.org/\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>OncoMX<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://cran.r-project.org/web/packages/methcon5/index.html\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>MethCon5<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://civicdb.org/home\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>Clinical Interpretation of Variants in Cancer (CIViC) Knowledgebase<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://hive.biochemistry.gwu.edu/biomuta\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>BioMuta<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://www.cancerimagingarchive.net/\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>The Cancer Imaging Archive (TCIA)<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://github.com/KrasnitzLab/SCGV\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>Single Cell Genome Viewer (SCGV)<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://vjcitn.shinyapps.io/ivyglimpse/\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>ivyGlimpse<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://tcpaportal.org/index.html\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>The Cancer Proteome Atlas<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://github.com/qiicr/dcmqi\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>dcmqi: DICOM for Quantitative Imaging<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://github.com/SBU-BMI/region-templates\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>Region Templates<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"http://cistrome.org/Cistrome/Cistrome_Project.html\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>Cistrome<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"http://www.topasmc.org/\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>TOPAS<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>The Cancer Genome Atlas (TCGA)<\/a><\/b>","<b><a href=\"https://www.internationalgenome.org/\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>1000 Genomes Project<\/a><\/b>","<b><a href=\"https://ocg.cancer.gov/programs/target\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> 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href=\"https://dcc.icgc.org/\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>ICGC Data Portal<\/a><\/b>","<b><a href=\"https://www.isic-archive.com/\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>ISIC Archive<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://cedar.iedb.org/\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>Cancer Epitope Database and Analysis Resource (CEDAR)<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://maayanlab.cloud/archs4/\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>ARCHS4<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>","<b><a href=\"https://portal.pedscommons.org/login\"style=\"color:#be3b2a\"target=\"_blank\"<div title=\"Main Link\"> <\/div>Pediatric Cancer Data Commons (PCDC)<\/a><\/b><br><\/br><img src=\"ITCRLogo.png\" height=\"40\"><\/img>"],["Genomics","Ontology","Genomics","Genomics","Genomics","Genomics","Genomics","Cancer Imaging","Genomics","Genomics","Proteomics","DICOM Standards, Cancer Imaging","Image Analysis","Genomics","Radiology Imaging","Genomics, Proteomics","Genomics","Genomics","Genomics, Proteomics","Genomics","Proteomics","Genomics, Algorithms","Genomics, Cancer Imaging","Genomics","Cancer Imaging","Proteomics","Transcriptomics","Clinical"],["PDX Finder is a freely available resource that is integrating, archiving and disseminating information about Patient Derived Xenograft (PDX) models and their associated data.","OMOP-formatted ontology of chemotherapy regimens, their component drugs, and supporting publications, with >87,000 concepts and nearly 240,000 relationships. A portion is available as the HemOnc vocabulary through the athena.ohdsi.org vocabulary management tool. The full ontology is freely available to academic and non-commercial users through the CC-BY-NC-SA 4.0 license; a drug-focused subset is available to any user through the CC-BY 4.0 license.","Next-Generation (Clustered) Heat Maps are interactive heat maps that enable the user to zoom and pan across the heatmap, alter its color scheme, generate production quality PDFs, and link out from rows, columns, and individual heatmap entries to related statistics, databases and other information.","OncoMX is a cancer biomarker database with mutation and expression metadata related to the study of cancer alongside relevant experimental and functional annotations.","The goal of methcon5 is to identify and rank CpG DNA methylation conservation along the human genome.","CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer. Our goal is to enable precision medicine by providing an educational forum for dissemination of knowledge and active discussion of the clinical significance of cancer genome alterations.","Cancer associated gene mutation","TCIA is NCI’s repository for publicly shared cancer imaging data. TCIA collections include radiology and pathology images, clinical and clinical trial data, image derived annotations and quantitative features and a growing collection of related ‘omics data both from clinical and pre-clinical studies.","Graphics user interface for single-cell genomics","Bioconductor-based interface to Ivy-GAP (glioblastoma.alleninstitute.org) data resources","The Cancer Proteome Atals is a comprehensive bioinformatic resource for assessing, visualzing and analyzing the functional proteomics data of patient tumor and cell line samples.","dcmqi is a free, open source library that implements conversion of the data stored in commonly used research formats into the standard DICOM representation","A suite of libraries and runtime to support image analysis.","Curated and processed human/mouse ChIP/DNase-seq datasets in GEO, allowing users to search, browse, download ChIP-seq data signals, peaks, QC, motifs, target genes and similar datasets.","Monte Carlo simulation of ionizing radiation transport for medical applications with focus on therapy and imaging with x-rays, electrons, protons and all other forms of ionizing radiation.","TCGA is one of the most comprehensive resources on cancer data with over 20,000 tumor and normal samples. There are 33 cancer types represented in this resource, and this resource remains one of the largest publically avaiable sources for cancer data in the reserach community.","The 1000 Genomes Project aimed to collect common genetic variants with frequencies of at least 1% in the populations studied. This project sequenced thousands of genomes to create a publically accessible database for researchers.","TARGET tracks genetic changes across several datasets in order to better understand reasons for the initiation and progression of several childhood cancers. The organization aims to make this information as freely accessible as possible to accelerate the development of novel solutions to pediatric cancer treatments.","Researchers initially developed the CCLE to create a series of datasets from 1000 human cancer models. The cell lines were expanded upon to include a series of SNP derived data, allowing for the testing of anti-cancer therapeutics on these cell lines. Over the years, these datasets were expanded upon to include NGS techniques to refine the characterization of mRNA expression within these cell lines. Lastly, the program aims to conduct a series of MS quantifications to determine the abundance of produced proteins.","This resource serves as a database of clinical study results that examine the intersection between genotype and phenotypes.","CPTAC focuses on proteogenomic analysis of colorectal, ovarian, and breast cancers within human cell lines. This involved the compilation of identified preoteomic-centric cancer subtypes, driver mutations, and cancer pathways.","PheKB is a collaborative resource that allows users to contribute electronic algorithms to identify various characteristics of patient health data. This resource contains a series of integrated tools and standardizations for the user-contributed data that is added to the resource.","This resource contains a selection of images from non-small cell lung cancer patients acquired through CT scans. All datasets were manually delineated by radiation oncologists while also containing clinical outcome data in addition to the raw imaging files.","This resource offers a suite of tools and datasets that allow for the visualization and retrieval of various cancer data.","The ISIC Archive is an academic-industry collaboration that is devoted to improving dermatology artificial intelligence. It is the largest public archive of images of skin conditions, with special attention to skin cancer detection. We also host grand challenges (and live challenges) for AI models as well as conference workshops.","The Cancer Epitope Database and Analysis Resource (CEDAR) is a freely available resource funded by NCI. It catalogs experimental data on antibody and T cell epitopes studied in humans, non-human primates, and other animal species in the context of cancer disease. CEDAR also hosts tools to assist in the prediction and analysis of cancer epitopes.","ARCHS4 provides gene and trasncript counts uniformly processed from all the human and mouse RNA-seq samples from GEO","The PCDC Data Portal offers a unified platform where researchers can use the cohort explorer and other analysis tools to explore available data and assess study feasibility; if a user wishes to perform research with data from the PCDC, the proposed project undergoes review and approval by the relevant disease consortium."],["Utilizes histopathological imagte data, molecular tumor classification, host strain metadata, and genomic data to create fully integrated visual models.","Open resource for all researchers to collaborate and explore curated datasets.","The data used in this resource are selected, standardized TCGA datasets.","Allows for a side-by-side comparison of experimental data and functional information.","Utilizes bootstrapping methods to rank CpG DNA Methylation conservation. Built to run with R.","All content is freely available, and users can easily contribute their own data to this resource.","Focuses explicitly on nonsynonymous single-nucleotide variations (nsSNVs).","Data is deidentified. Data can be serached through collections searched by disease, image modality, and research focus. Uses DICOM file format.","Involves the local installation of Anaconda.","Specifically examines data for glioplastoma patients. Allows for a direct comparison of datasets.","Data contains modules for both analysis and visualization.","Lightweight collection of tools and resources with minimal dependencies. Promotes standardization through DICOM","Highly technical setup to utilize the suite of image analysis tools.","Contains CRISPR tools for data analysis; other tools available for use","This resource models x-ray and particle therapy treatment heads, patient geometry, and replays phase space. With the correct set of inputs and data, this resource allows for easily accessible and reproducible modeling outputs.","TCGA functions through the Genomic Data Commons, allowing for direct comparisons with data found in other GDC datasets.","1000 Genomes Project is one of the largest continuously updated genomics resources available to researchers","Contains data collected from acute myeloid leukemia, osteosarcoma, kidney tumors, acute lymphoblastic leukemia, and neuroblastoma","Contains a series of deep examinations of several cancer cell lines, allowing for a comprehensive examination of specific datasets.","This resource contains a broad archive of human genomic data.","Focuses specifically on colorectal, breast, and ovarian cancer.","This resource contains a set of tools that allow for cross-site collaboration from algorithm development, validation, and sharing.","Focuses specifically on non-small cell lung cancer imaging","This resource is developed explicitly to work with the Overture Platform","The largest public archive of dermatology photographs. It has around 20 million individual image downloads per month and is widely used for education and AI research.","It is a free resoure that provides the cancer community with a central repository of experimentally-tested cancer epitopes curated from peer-reviewed literature.","This resource is updated frequently. It contains all GEO samples and includes metadata and data search.","Uses consensus-based data dictionaries and maps all clinical data in the portal to standardized terms; provides a data portal and analysis tools to assess study feasibility"],["Xenograft Models, PDF Models","Cancer Publications","Clustered Heat Maps","Biomarkers, Genes","Methylation Data","Precision Medicine Library","SNV Datasets, Sequence Data","MRI, CT, Histopathology","Single-Cell Genomics","Imaging Data","Cancer Cell Lines, Patient Cohorts, Perturbed Proteomics","Segmentation Imaging, Parametric Map Imaging, Columetric Measurements","Imaging Data","Cistrome Anaysis","X-Ray, Particle Therapy, CT Imaging, Score Dose, Fluence","Clinical, Copy Number, DNA, Imaging, Methylation, Microsatellite Instability, miRNA, mRNA Expression, Protein Expression","Genomic Sequences, Genotype Variations","Genomic Sequences, Transcriptome Data","Cancer Cell Lines","Genomic Sequences","Cancer Cell Lines","Clinical, Algorithms","Clinical, Imaging Data","Algorithms, Genomic Seuqnces, Cancer Pathway Data","Clinical imaging","Curated literature data: experimentally-tested epitopes and their immunological, biological, and clinical contexts","Transcriptomics, GEO","ALL Data Commons, C3P, CHIC, FA Data Commons, Global REACH, HIBiSCus, INRG, INSPiRE, INSTRuCT, INTERACT, MaGIC, NOBLE, NODAL, Reproductive HOPE"],["Free","Free","Free","Free","Free","Free","Free","Free","Free","Free","Free","Free","Free","Free","<a href=\"https://www.topasmc.org/license\" style=\"color: #be3b2a\" target=\"_blank\"<div title=\"Pricing Link\"> <\/div>Paid/Free<\/a>","Free","Free","Free","Free","Free","Free","Free","Free","Free","Free","Free","Free for academic institutions","Free"]],"container":"<table class=\"display\">\n <thead>\n <tr>\n <th>Name<\/th>\n <th>Subcategories<\/th>\n <th>Summary<\/th>\n <th>Unique Factor<\/th>\n <th>Types of Data<\/th>\n <th>Price<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"scrollX":true,"autoWidth":true,"pageLength":10,"scrollCollapse":true,"fillContainer":true,"order":[0,"asc"],"columnDefs":[{"className":"dt-center","targets":"_all"},{"width":"120px","targets":0},{"width":"300px","targets":2},{"width":"140px","targets":3},{"width":"100px","targets":4}],"initComplete":"function(settings, json) {\n$(this.api().table().header()).css({'backgroundColor': '#3f546f'});\n$(this.api().table().header()).css({'color': '#fff'});\n}","orderClasses":false,"orderCellsTop":true}},"evals":["options.initComplete"],"jsHooks":[]}</script>
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