Package Recipe 'bioconductor-mutationalpatterns'

recipe bioconductor-mutationalpatterns

Comprehensive genome-wide analysis of mutational processes

Homepage:: https://bioconductor.org/packages/3.20/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¶

Versions:

3.19.1-0, 3.16.0-0, 3.12.0-0, 3.10.0-0, 3.8.0-0, 3.4.0-0, 3.2.0-0, 3.0.1-0, 3.0.0-0,

3.19.1-0, 3.16.0-0, 3.12.0-0, 3.10.0-0, 3.8.0-0, 3.4.0-0, 3.2.0-0, 3.0.1-0, 3.0.0-0, 2.0.0-0, 1.12.0-0, 1.10.0-1, 1.8.0-0, 1.6.1-0, 1.4.3-0, 1.4.1-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-bsgenome >=1.78.0,<1.79.0
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-variantannotation >=1.56.0,<1.57.0
on r-base >=4.5,<4.6.0a0
on r-cowplot >=0.9.2
on r-dplyr >=0.8.3
on r-ggalluvial >=0.12.2
on r-ggdendro >=0.1-20
on r-ggplot2 >=2.1.0
on r-magrittr >=1.5
on r-nmf >=0.20.6
on r-pracma >=1.8.8
on r-purrr >=0.3.2
on r-rcolorbrewer
on r-stringr >=1.4.0
on r-tibble >=2.1.3
on r-tidyr >=1.0.0

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-mutationalpatterns

to add into an existing workspace instead, run:

pixi add bioconductor-mutationalpatterns

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-mutationalpatterns

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-mutationalpatterns

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

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-mutationalpatterns/README.html)