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:

0.1.3-0,  0.1.2-0

Depends:

• bioconductor-biocgenerics

• bioconductor-clusterprofiler

• bioconductor-maftools

• r-base >=4.1,<4.2.0a0

• r-caret

• r-data.table

• r-glmnet

• r-proc

• r-purrr

• r-randomforest

• r-rcolorbrewer

• r-survival

• r-survminer

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install r-pathwaytmb

and update with:

conda update r-pathwaytmb

or use the docker container:

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

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

Download stats

Link to this page

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