recipe bioconductor-decomptumor2sig

Decomposition of individual tumors into mutational signatures by signature refitting

Homepage

https://bioconductor.org/packages/3.11/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

2.4.0-0, 2.2.0-0, 2.0.0-1

Depends

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-biostrings >=2.56.0,<2.57.0

• bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0

• bioconductor-genomicfeatures >=1.40.0,<1.41.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-s4vectors >=0.26.0,<0.27.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0

• bioconductor-variantannotation >=1.34.0,<1.35.0

• r-base >=4.0,<4.1.0a0

• r-data.table

• r-ggplot2

• r-ggseqlogo

• r-gridextra

• r-matrix

• r-plyr

• r-quadprog >=1.5-5

• r-vcfr

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-decomptumor2sig

and update with:

conda update bioconductor-decomptumor2sig

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-decomptumor2sig:<tag>

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

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)