recipe bioconductor-meskit

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

Homepage:

https://bioconductor.org/packages/3.18/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:

1.12.0-0,  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 bioconductor-annotationdbi:

>=1.64.0,<1.65.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-ape:

>=5.4.1

depends r-base:

>=4.3,<4.4.0a0

depends r-circlize:

depends r-cowplot:

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-ggrepel:

depends r-ggridges:

depends r-mclust:

depends r-phangorn:

depends r-pracma:

depends r-rcolorbrewer:

depends r-tidyr:

>=1.0.0

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-meskit

and update with::

   mamba update bioconductor-meskit

To create a new environment, run:

mamba create --name myenvname bioconductor-meskit

with myenvname being 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-meskit:<tag>

(see `bioconductor-meskit/tags`_ for valid values for ``<tag>``)

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