recipe bioconductor-rtcga

The Cancer Genome Atlas Data Integration







biotools: rtcga, doi: 10.1038/nmeth.3252

The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients' treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.

package bioconductor-rtcga

(downloads) docker_bioconductor-rtcga



depends r-assertthat:

depends r-base:


depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-ggthemes:

depends r-htmltools:

depends r-knitr:

depends r-purrr:

depends r-rcurl:

depends r-rmarkdown:

depends r-rvest:

depends r-scales:

depends r-stringi:

depends r-survival:

depends r-survminer:

depends r-viridis:

depends r-xml:

depends r-xml2:



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-rtcga

and update with::

   mamba update bioconductor-rtcga

To create a new environment, run:

mamba create --name myenvname bioconductor-rtcga

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<tag>

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

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