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GDC RNASeq Tool

Data AccessData Analysis
Authors: Colin Reid, GDC User Services| Posted Date:

The GDC RNASeq Tool downloads / merges individual RNASeq files from the GDC Data Portal into a matrices identified by TCGA barcode.

The GDC RNASeq Tool:

  • Downloads RNA-Seq / miRNA-Seq data files using a GDC manifest file
  • Unzips the files into separate folders identified by experimental strategy and bioinformatics workflow
  • Merges the files into separate matrix files

GenomicDataCommons R-Package

Data AccessData Analysis
Authors: | Posted Date:

The National Cancer Institute (NCI) Genomic Data Commons provides the cancer research community with an open and unified repository for sharing and accessing data across numerous cancer studies and projects via a high-performance data transfer and query infrastructure. The Bioconductor project is an open source and open development software project built on the R statistical programming environment. A major goal of the Bioconductor project is to facilitate the use, analysis, and comprehension of genomic data. The GenomicDataCommons Bioconductor package provides basic infrastructure for querying, accessing, and mining genomic datasets available from the GDC. We expect that Bioconductor developer and bioinformatics community will build on the GenomicDataCommons package to add higher-level functionality and expose cancer genomics data to many state-of-the-art bioinformatics methods available in Bioconductor.

TCGABiolinks

Data AccessData Analysis
Authors: Tiago Chedraoui Silva, Antonio Colaprico, Catharina Olsen, Michele Ceccarelli, Gianluca Bontempi, Houtan Noushmehr| Posted Date:

TCGAbiolinks was developed as an R/Bioconductor to address challenges with data mining and analysis of cancer genomics data stored at GDC. We offer bioinformatics solutions by using a guided workflow to allow users to query, download, and perform integrative analyses of GDC data. We combined methods from computer science and statistics into the pipeline and incorporated methodologies developed in previous TCGA marker studies. We also provide a graphics user interface (GUI) version of TCGAbiolinks that can run on a user's local machine. TCGAbiolinksGUI contains all the features of the R-version yet allows users an easier way to navigate the analysis steps. We provide online documentations, tutorials, and video guides to assist users with the analysis.