Package Recipe 'bioconductor-rtcgatoolbox'

recipe bioconductor-rtcgatoolbox

A new tool for exporting TCGA Firehose data

Homepage:: https://bioconductor.org/packages/3.20/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:

2.40.0-0, 2.36.0-0, 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,

2.40.0-0, 2.36.0-0, 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:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-delayedarray >=0.36.0,<0.37.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-raggedexperiment >=1.34.0,<1.35.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-tcgautils >=1.30.0,<1.31.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-httr
on r-rcurl
on r-rjsonio
on r-rvest
on r-stringr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-rtcgatoolbox

to add into an existing workspace instead, run:

pixi add bioconductor-rtcgatoolbox

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-rtcgatoolbox

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-rtcgatoolbox

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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)