library(GenomicDataCommons) Check basic functionality status()#> $commit#> [1] "4dd3680528a19ed33cfc83c7d049426c97bb903b"#>#> $data_release#> [1] "Data Release 34.0 - July 27, 2022"#>#> $status#> [1] "OK"#>#> $tag#> [1] "3.0.0"#>#> $version#> [1] 1 ...
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 research. The proteogenomic data generated ...
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...
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 ...
The goal of the National Cancer Institute's (NCI's) Genomic Data Commons (GDC) is to provide the cancer research community with a data repository of uniformly processed genomic and associated clinical data that enables data sharing and collaborative analysis in the support of precision medicine. ...
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002;30:325–7. Article CAS PubMed PubMed Central Google Scholar Guo Z, Kuang Z, Zhao Y, Deng Y, He H, Wan M et al. PmiREN2.0: ...
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 used for analyses described in this manuscript were obtained fromhttps://portal.gdc.cancer.gov/. All the accession files used to download data are available athttps://github.com/Kingsford-Group/variantstore/tree/master/eval_data_records/gdc_manifest. The script used to download the TCGA ...
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...
900 LC-MS/MS runs, and a total of 31,231,980 MS/MS spectra. Somatic variants and germline variants for colon cancer samples were from the original publication10. Somatic variants and germline variants for breast cancer samples were downloaded from the genomic data commons (GDC,https://portal...