recipe bioconductor-decomptumor2sig

Decomposition of individual tumors into mutational signatures by signature refitting

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/decompTumor2Sig.html

License:

GPL-2

Recipe:

/bioconductor-decomptumor2sig/meta.yaml

Uses quadratic programming for signature refitting, i.e., to decompose the mutation catalog from an individual tumor sample into a set of given mutational signatures (either Alexandrov-model signatures or Shiraishi-model signatures), computing weights that reflect the contributions of the signatures to the mutation load of the tumor.

package bioconductor-decomptumor2sig

versions:

2.16.0-0,  2.14.0-0,  2.10.0-0,  2.8.0-0,  2.6.0-1,  2.6.0-0,  2.4.0-0,  2.2.0-0,  2.0.0-1

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-bsgenome.hsapiens.ucsc.hg19:

>=1.4.0,<1.5.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:

>=3.2.0,<3.3.0

depends bioconductor-variantannotation:

>=1.46.0,<1.47.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-ggplot2:

depends r-ggseqlogo:

depends r-gridextra:

depends r-matrix:

depends r-plyr:

depends r-quadprog:

>=1.5-5

depends r-readxl:

requirements:

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-decomptumor2sig

and update with::

   mamba update bioconductor-decomptumor2sig

To create a new environment, run:

mamba create --name myenvname bioconductor-decomptumor2sig

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-decomptumor2sig:<tag>

(see `bioconductor-decomptumor2sig/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an 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-decomptumor2sig/README.html)