Package Recipe 'bioconductor-musicatk'

recipe bioconductor-musicatk

Mutational Signature Comprehensive Analysis Toolkit

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/musicatk.html
License:: LGPL-3
Recipe:: /bioconductor-musicatk/meta.yaml

Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3.

package bioconductor-musicatk¶

Versions:

2.4.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-0, 1.4.0-0, 1.2.0-0, 1.0.0-2, 1.0.0-1

Depends:

on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-bsgenome >=1.78.0,<1.79.0
on bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0
on bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0
on bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0
on bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-decomptumor2sig >=2.26.0,<2.27.0
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-maftools >=2.26.0,<2.27.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.22.0,<3.23.0
on bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.22.0,<3.23.0
on bioconductor-variantannotation >=1.56.0,<1.57.0
on r-base >=4.5,<4.6.0a0
on r-cluster
on r-data.table
on r-dplyr
on r-factoextra
on r-ggplot2
on r-ggpubr
on r-ggrepel
on r-gridextra
on r-gtools
on r-magrittr
on r-mass
on r-matrix >=1.6.1
on r-matrixtests
on r-mcmcprecision
on r-nmf
on r-philentropy
on r-plotly
on r-rlang
on r-scales
on r-shiny
on r-stringi
on r-stringr
on r-tibble
on r-tidyr
on r-tidyverse
on r-topicmodels
on r-uwot

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-musicatk

to add into an existing workspace instead, run:

pixi add bioconductor-musicatk

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-musicatk

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-musicatk

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-musicatk:<tag>

(see bioconductor-musicatk/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-musicatk/README.html)