recipe bioconductor-camutqc

An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/CaMutQC.html

License:

GPL-3

Recipe:

/bioconductor-camutqc/meta.yaml

CaMutQC is able to filter false positive mutations generated due to technical issues, as well as to select candidate cancer mutations through a series of well-structured functions by labeling mutations with various flags. And a detailed and vivid filter report will be offered after completing a whole filtration or selection section. Also, CaMutQC integrates serveral methods and gene panels for Tumor Mutational Burden (TMB) estimation.

package bioconductor-camutqc

(downloads) docker_bioconductor-camutqc

versions:

1.2.0-0

depends bioconductor-clusterprofiler:

>=4.14.0,<4.15.0

depends bioconductor-maftools:

>=2.22.0,<2.23.0

depends bioconductor-meskit:

>=1.16.0,<1.17.0

depends bioconductor-org.hs.eg.db:

>=3.20.0,<3.21.0

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

depends r-dplyr:

depends r-dt:

depends r-ggplot2:

depends r-stringr:

depends r-tidyr:

depends r-vcfr:

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 bioconductor-camutqc

and update with::

   mamba update bioconductor-camutqc

To create a new environment, run:

mamba create --name myenvname bioconductor-camutqc

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/bioconductor-camutqc:<tag>

(see `bioconductor-camutqc/tags`_ for valid values for ``<tag>``)

Download stats

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/bioconductor-camutqc/README.html)