- recipe bioconductor-pcxndata
Correlation coefficients and p values between pre-defined pathway/gene sets
MIT + file LICENSE
PCxN database contains correlation coefficients and p values between pre-defined gene sets within MSigDB H hallmark gene sets, MSigDB C2 CP (Canonical pathways), MSigDB C5 GO BP gene sets and Pathprint respectively, as well as adjusted pathway correlations to account for the shared genes between pathway pairs.
- package bioconductor-pcxndata¶
- depends bioconductor-data-packages:
- depends curl:
- depends r-base:
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-pcxndata and update with:: mamba update bioconductor-pcxndata
To create a new environment, run:
mamba create --name myenvname bioconductor-pcxndata
myenvnamebeing 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-pcxndata:<tag> (see `bioconductor-pcxndata/tags`_ for valid values for ``<tag>``)