recipe bioconductor-rtcgatoolbox

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.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/RTCGAToolbox.html

License

file LICENSE

Recipe

/bioconductor-rtcgatoolbox/meta.yaml

Links

biotools: rtcgatoolbox

package bioconductor-rtcgatoolbox

(downloads) docker_bioconductor-rtcgatoolbox

Versions

2.12.1-0, 2.10.0-0, 2.8.0-0, 2.6.0-0

Depends bioconductor-biocgenerics

>=0.28.0,<0.29.0

Depends bioconductor-delayedarray

>=0.8.0,<0.9.0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-limma

>=3.38.0,<3.39.0

Depends bioconductor-raggedexperiment

>=1.6.0,<1.7.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends bioconductor-tcgautils

>=1.2.0,<1.3.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-data.table

Depends r-rcircos

Depends r-rcurl

Depends r-rjsonio

Depends r-stringr

Depends r-survival

Depends r-xml

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-rtcgatoolbox

and update with:

conda update bioconductor-rtcgatoolbox

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-rtcgatoolbox:<tag>

(see bioconductor-rtcgatoolbox/tags for valid values for <tag>)

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-rtcgatoolbox/README.html)