DOI: 10.18129/B9.bioc.RTCGAToolbox    

A new tool for exporting TCGA Firehose data

Bioconductor version: Release (3.6)

Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.

Author: Mehmet Kemal Samur

Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>

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biocViews DifferentialExpression, GeneExpression, Sequencing, Software
Version 2.8.0
In Bioconductor since BioC 3.2 (R-3.2) (2.5 years)
License file LICENSE
Depends R (>= 3.4.0)
Imports Biobase, BiocGenerics, data.table (>= 1.9.4), GenomicRanges, GenomeInfoDb, httr, IRanges, limma(>= 3.18), methods, plyr, RaggedExperiment, RCircos, RCurl, RJSONIO, S4Vectors, SummarizedExperiment, survival, XML
Suggests BiocStyle, Homo.sapiens, knitr, MultiAssayExperiment, readr, rmarkdown
URL http://mksamur.github.io/RTCGAToolbox/
BugReports https://github.com/mksamur/RTCGAToolbox/issues
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Source Package RTCGAToolbox_2.8.0.tar.gz
Windows Binary RTCGAToolbox_2.8.0.zip
Mac OS X 10.11 (El Capitan) RTCGAToolbox_2.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RTCGAToolbox
Package Short Url http://bioconductor.org/packages/RTCGAToolbox/
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