recipe bioconductor-sigspack

Mutational Signature Estimation for Single Samples

Homepage

https://bioconductor.org/packages/3.11/bioc/html/SigsPack.html

License

GPL-3

Recipe

/bioconductor-sigspack/meta.yaml

Single sample estimation of exposure to mutational signatures. Exposures to known mutational signatures are estimated for single samples, based on quadratic programming algorithms. Bootstrapping the input mutational catalogues provides estimations on the stability of these exposures. The effect of the sequence composition of mutational context can be taken into account by normalising the catalogues.

package bioconductor-sigspack

Versions

1.2.0-0, 1.0.0-0

Depends

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-biostrings >=2.56.0,<2.57.0

• bioconductor-bsgenome >=1.56.0,<1.57.0

• bioconductor-genomeinfodb >=1.24.0,<1.25.0

• bioconductor-genomicranges >=1.40.0,<1.41.0

• bioconductor-rtracklayer >=1.48.0,<1.49.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• bioconductor-variantannotation >=1.34.0,<1.35.0

• r-base >=4.0,<4.1.0a0

• r-quadprog >=1.5-5

Required By

Installation

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

conda install bioconductor-sigspack

and update with:

conda update bioconductor-sigspack

or use the docker container:

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

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

Link to this page

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