recipe r-ggcoverage

The goal of 'ggcoverage' is to simplify the process of visualizing genome coverage. It contains functions to load data from BAM, BigWig or BedGraph files, create genome coverage plot, add various annotations to the coverage plot, including base and amino acid annotation, GC annotation, gene annotation, transcript annotation, ideogram annotation and peak annotation.

Homepage:

https://CRAN.R-project.org/package=ggcoverage

License:

MIT / MIT

Recipe:

/r-ggcoverage/meta.yaml

package r-ggcoverage

versions:

0.7.1-2,  0.7.1-1,  0.7.1-0,  0.7.0-0

depends bioconductor-biostrings:

depends bioconductor-bsgenome:

depends bioconductor-genomeinfodb:

depends bioconductor-genomicalignments:

depends bioconductor-genomicranges:

depends bioconductor-ggbio:

depends bioconductor-iranges:

depends bioconductor-rsamtools:

depends bioconductor-rtracklayer:

depends bioconductor-s4vectors:

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggh4x:

depends r-ggplot2:

depends r-ggrepel:

depends r-magrittr:

depends r-patchwork:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-rlang:

depends r-scales:

depends r-seqinr:

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 r-ggcoverage

and update with::

   mamba update r-ggcoverage

To create a new environment, run:

mamba create --name myenvname r-ggcoverage

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/r-ggcoverage:<tag>

(see `r-ggcoverage/tags`_ for valid values for ``<tag>``)

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