recipe bioconductor-rtcgatoolbox

A new tool for exporting TCGA Firehose data

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/RTCGAToolbox.html

License:

GPL-2

Recipe:

/bioconductor-rtcgatoolbox/meta.yaml

Links:

biotools: 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.

package bioconductor-rtcgatoolbox

versions:

2.32.1-0,  2.30.0-0,  2.28.0-0,  2.24.0-0,  2.22.0-0,  2.20.0-1,  2.20.0-0,  2.18.0-0,  2.16.0-0, 

2.32.1-0,  2.30.0-0,  2.28.0-0,  2.24.0-0,  2.22.0-0,  2.20.0-1,  2.20.0-0,  2.18.0-0,  2.16.0-0,  2.14.0-1,  2.12.1-0,  2.10.0-0,  2.8.0-0,  2.6.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-raggedexperiment:

>=1.26.0,<1.27.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-tcgautils:

>=1.22.0,<1.23.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-httr:

depends r-rcurl:

depends r-rjsonio:

depends r-rvest:

depends r-stringr:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-rtcgatoolbox

and update with::

   mamba update bioconductor-rtcgatoolbox

To create a new environment, run:

mamba create --name myenvname bioconductor-rtcgatoolbox

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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