- 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:
- License:
MIT / MIT
- Recipe:
- package r-ggcoverage¶
- Versions:
0.7.1-3,0.7.1-2,0.7.1-1,0.7.1-0,0.7.0-0- Depends:
on bioconductor-biostrings
on bioconductor-bsgenome
on bioconductor-genomeinfodb
on bioconductor-genomicalignments
on bioconductor-genomicranges
on bioconductor-ggbio
on bioconductor-iranges
on bioconductor-rsamtools
on bioconductor-rtracklayer
on bioconductor-s4vectors
on r-base
>=4.4,<4.5.0a0on r-dplyr
on r-ggh4x
on r-ggplot2
on r-ggrepel
on r-magrittr
on r-patchwork
on r-rcolorbrewer
on r-reshape2
on r-rlang
on r-scales
on r-seqinr
- 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 r-ggcoverage
to add into an existing workspace instead, run:
pixi add r-ggcoverage
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 r-ggcoverage
Alternatively, to install into a new environment, run:
conda create -n envname r-ggcoverage
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/r-ggcoverage:<tag>
(see r-ggcoverage/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:
[](http://bioconda.github.io/recipes/r-ggcoverage/README.html)
