recipe bioconductor-mutationalpatterns

Comprehensive genome-wide analysis of mutational processes

Homepage

https://bioconductor.org/packages/3.13/bioc/html/MutationalPatterns.html

License

MIT + file LICENSE

Recipe

/bioconductor-mutationalpatterns/meta.yaml

Mutational processes leave characteristic footprints in genomic DNA. This package provides a comprehensive set of flexible functions that allows researchers to easily evaluate and visualize a multitude of mutational patterns in base substitution catalogues of e.g. healthy samples, tumour samples, or DNA-repair deficient cells. The package covers a wide range of patterns including: mutational signatures, transcriptional and replicative strand bias, lesion segregation, genomic distribution and association with genomic features, which are collectively meaningful for studying the activity of mutational processes. The package works with single nucleotide variants (SNVs), insertions and deletions (Indels), double base substitutions (DBSs) and larger multi base substitutions (MBSs). The package provides functionalities for both extracting mutational signatures de novo and determining the contribution of previously identified mutational signatures on a single sample level. MutationalPatterns integrates with common R genomic analysis workflows and allows easy association with (publicly available) annotation data.

package bioconductor-mutationalpatterns

(downloads) docker_bioconductor-mutationalpatterns

Versions
3.2.0-03.0.1-03.0.0-02.0.0-01.12.0-01.10.0-11.8.0-01.6.1-01.4.3-0

3.2.0-03.0.1-03.0.0-02.0.0-01.12.0-01.10.0-11.8.0-01.6.1-01.4.3-01.4.1-0

Depends
Required By

Installation

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

conda install bioconductor-mutationalpatterns

and update with:

conda update bioconductor-mutationalpatterns

or use the docker container:

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

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