- 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:
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-quadprog
>=1.5-5
- Required By:
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¶
Render an badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-decomptumor2sig/README.html)