recipe bioconductor-geotcgadata

Processing Various Types of Data on GEO and TCGA






Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.

package bioconductor-geotcgadata

(downloads) docker_bioconductor-geotcgadata



depends bioconductor-cqn:


depends bioconductor-summarizedexperiment:


depends bioconductor-topconfects:


depends r-base:


depends r-data.table:

depends r-plyr:



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-geotcgadata

and update with::

   mamba update bioconductor-geotcgadata

To create a new environment, run:

mamba create --name myenvname bioconductor-geotcgadata

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-geotcgadata/tags`_ for valid values for ``<tag>``)

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