Package Recipe 'bioconductor-meskit'

recipe bioconductor-meskit

A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/MesKit.html
License:: GPL-3
Recipe:: /bioconductor-meskit/meta.yaml

MesKit provides commonly used analysis and visualization modules based on mutational data generated by multi-region sequencing (MRS). This package allows to depict mutational profiles, measure heterogeneity within or between tumors from the same patient, track evolutionary dynamics, as well as characterize mutational patterns on different levels. Shiny application was also developed for a need of GUI-based analysis. As a handy tool, MesKit can facilitate the interpretation of tumor heterogeneity and the understanding of evolutionary relationship between regions in MRS study.

package bioconductor-meskit¶

Versions:

1.20.0-0, 1.16.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-0, 1.4.0-0, 1.2.0-0, 1.0.1-0, 1.0.0-0,

1.20.0-0, 1.16.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-0, 1.4.0-0, 1.2.0-0, 1.0.1-0, 1.0.0-0, 0.99.16-0

Depends:

on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on r-ape >=5.4.1
on r-base >=4.5,<4.6.0a0
on r-circlize
on r-cowplot
on r-data.table
on r-dplyr
on r-ggplot2
on r-ggrepel
on r-ggridges
on r-mclust
on r-phangorn
on r-pracma
on r-rcolorbrewer
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-meskit

to add into an existing workspace instead, run:

pixi add bioconductor-meskit

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-meskit

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-meskit

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-meskit:<tag>

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