recipe r-pathwaytmb

A systematic bioinformatics tool to develop a new pathway-based gene panel for tumor mutational burden (TMB) assessment (pathway-based tumor mutational burden, PTMB), using somatic mutations files in an efficient manner from either The Cancer Genome Atlas sources or any in-house studies as long as the data is in mutation annotation file (MAF) format. Besides, we develop a multiple machine learning method using the sample's PTMB profiles to identify cancer-specific dysfunction pathways, which can be a biomarker of prognostic and predictive for cancer immunotherapy.

Homepage:

https://CRAN.R-project.org/package=pathwayTMB

License:

GPL2 / GPL-2.0-or-later

Recipe:

/r-pathwaytmb/meta.yaml

package r-pathwaytmb

versions:

0.1.3-2,  0.1.3-1,  0.1.3-0,  0.1.2-0

depends bioconductor-biocgenerics:

depends bioconductor-clusterprofiler:

depends bioconductor-maftools:

depends r-base:

>=4.3,<4.4.0a0

depends r-caret:

depends r-data.table:

depends r-glmnet:

depends r-proc:

depends r-purrr:

depends r-randomforest:

depends r-rcolorbrewer:

depends r-survival:

depends r-survminer:

requirements:

additional platforms:

Installation

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 r-pathwaytmb

and update with::

   mamba update r-pathwaytmb

To create a new environment, run:

mamba create --name myenvname r-pathwaytmb

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 quay.io/biocontainers/r-pathwaytmb:<tag>

(see `r-pathwaytmb/tags`_ for valid values for ``<tag>``)

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