First, create adata.framefrom the clinical data: expands<-c("diagnoses","annotations","demographic","exposures")clinResults<-cases()|>GenomicDataCommons::select(NULL)|>GenomicDataCommons::expand(expands)|>results(size=6)demoDF<-filterAllNA(clinResults$demographic)exposuresDF<-bindrowname(clinResult...
In this paper, we describe the pipelines and workflows used to process and harmonize the data in the GDC. The generated data, as well as the original input files from TCGA and TARGET, are available for download and exploratory analysis at the GDC Data Portal and Legacy Archive ( https://...
National Cancer Institute Data Commons The Genomic Data Commons (GDC, https://portal.gdc.cancer.gov) and Proteomic Data Commons (PDC, https://pdc.cancer.gov) are National Cancer Institute (NCI) Cloud resources that coordinate storage and analysis of genomics and proteomics data for cancer researc...
We included WGS data from 100 NSCLC patients (50 AD and 50 SCC) from TCGA project (Genomic Data Commons Data Portal:https://portal.gdc.cancer.gov/) and downloaded the aligned “bam” files for following analysis. Processing of genomic data Somatic substitutions and indels were detected using ...
Analysis of TCGA PCPG Expression data Upper Quantile normalized FPKM (FPKM-UQ) gene expression data for the TCGA Pheochromocytoma&Paraganglioma cohort were obtained from the Genomics Data Commons portal (https://gdc-portal.nci.nih.gov). Expression values for genes of interest were extracted and sum...
1. Downloading TCGA Data To download diagnostic WSIs (formatted as .svs files), molecular feature data and other clinical metadata, please refer to theNIH Genomic Data Commons Data Portaland thecBioPortal. WSIs for each cancer type can be downloaded using theGDC Data Transfer Tool. ...
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Prostate cancer dataset from a study performed at the Memorial Sloan Kettering Cancer Center (http://cbio.mskcc.org/). The samples in these datasets correspond to patient prostate cancer tumors. The MSKCC Cancer Genomics data portal (http://cbio.mskcc.org/cancergenomics/prostate/data/) was acces...
Data availability The primary and processed data used to generate the analyses presented here can be downloaded from the TCGA manuscript publication page, (https://tcga-data.nci.nih.gov/docs/publications/esca_2016), and from the Genomic Data Commons (https://gdc-portal.nci.nih.gov/legacy-archi...
Three large-scale proteomics data sets from a colon cancer study10and a breast cancer study7were downloaded from the CPTAC data portal, including a colon cancer label-free data set (https://cptac-data-portal.georgetown.edu/cptac/s/S037), a colon cancer TMT data set (https://cptac-data-...