Package Recipe 'bioconductor-decomptumor2sig'

recipe bioconductor-decomptumor2sig

Decomposition of individual tumors into mutational signatures by signature refitting

Homepage:: https://bioconductor.org/packages/3.16/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:

2.14.0-0, 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 >=0.44.0,<0.45.0
bioconductor-biostrings >=2.66.0,<2.67.0
bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0
bioconductor-genomeinfodb >=1.34.0,<1.35.0
bioconductor-genomicfeatures >=1.50.0,<1.51.0
bioconductor-genomicranges >=1.50.0,<1.51.0
bioconductor-s4vectors >=0.36.0,<0.37.0
bioconductor-summarizedexperiment >=1.28.0,<1.29.0
bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0
bioconductor-variantannotation >=1.44.0,<1.45.0
r-base >=4.2,<4.3.0a0
r-data.table
r-ggplot2
r-ggseqlogo
r-gridextra
r-matrix
r-plyr
r-quadprog >=1.5-5
r-readxl

Required By:

bioconductor-musicatk

Installation

With an activated Bioconda channel (see 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>)

Download stats¶

Link to this page¶

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