:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'r-pathwaytmb' .. highlight: bash r-pathwaytmb ============ .. conda:recipe:: r-pathwaytmb :replaces_section_title: :noindex: 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 `_ .. conda:package:: r-pathwaytmb |downloads_r-pathwaytmb| |docker_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: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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: (see `r-pathwaytmb/tags`_ for valid values for ````) .. |downloads_r-pathwaytmb| image:: https://img.shields.io/conda/dn/bioconda/r-pathwaytmb.svg?style=flat :target: https://anaconda.org/bioconda/r-pathwaytmb :alt: (downloads) .. |docker_r-pathwaytmb| image:: https://quay.io/repository/biocontainers/r-pathwaytmb/status :target: https://quay.io/repository/biocontainers/r-pathwaytmb .. _`r-pathwaytmb/tags`: https://quay.io/repository/biocontainers/r-pathwaytmb?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/r-pathwaytmb/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/r-pathwaytmb/README.html