The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.
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
Given that you already have a conda environment in which you want to have this package, install with: