- recipe bioconductor-musicatk
Mutational Signature Comprehensive Analysis Toolkit
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/musicatk.html
- License:
LGPL-3
- Recipe:
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:
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 bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-bsgenome:
>=1.70.0,<1.71.0- depends bioconductor-bsgenome.hsapiens.ucsc.hg19:
>=1.4.0,<1.5.0- depends bioconductor-bsgenome.hsapiens.ucsc.hg38:
>=1.4.0,<1.5.0- depends bioconductor-bsgenome.mmusculus.ucsc.mm10:
>=1.4.0,<1.5.0- depends bioconductor-bsgenome.mmusculus.ucsc.mm9:
>=1.4.0,<1.5.0- depends bioconductor-complexheatmap:
>=2.18.0,<2.19.0- depends bioconductor-decomptumor2sig:
>=2.18.0,<2.19.0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomicfeatures:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-maftools:
>=2.18.0,<2.19.0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:
>=3.2.0,<3.3.0- depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene:
>=3.18.0,<3.19.0- depends bioconductor-variantannotation:
>=1.48.0,<1.49.0- depends r-base:
>=4.3,<4.4.0a0- depends r-cluster:
- depends r-data.table:
- depends r-deconstructsigs:
- depends r-dplyr:
- depends r-factoextra:
- depends r-ggplot2:
- depends r-ggpubr:
- depends r-ggrepel:
- depends r-gridextra:
- depends r-gtools:
- depends r-magrittr:
- depends r-mass:
- depends r-matrixtests:
- depends r-mcmcprecision:
- depends r-nmf:
- depends r-philentropy:
- depends r-plotly:
- depends r-rlang:
- depends r-shiny:
- depends r-stringi:
- depends r-stringr:
- depends r-tibble:
- depends r-tidyr:
- depends r-tidyverse:
- depends r-topicmodels:
- depends r-uwot:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-musicatk and update with:: mamba update bioconductor-musicatk
To create a new environment, run:
mamba create --name myenvname bioconductor-musicatk
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-musicatk:<tag> (see `bioconductor-musicatk/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-musicatk/README.html)
