Package Recipe 'bioconductor-ggmsa'

recipe bioconductor-ggmsa

Plot Multiple Sequence Alignment using 'ggplot2'

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/ggmsa.html
License:: Artistic-2.0
Recipe:: /bioconductor-ggmsa/meta.yaml

A visual exploration tool for multiple sequence alignment and associated data. Supports MSA of DNA, RNA, and protein sequences using 'ggplot2'. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as phylogenetic tree Visualized by 'ggtree', boxplot, genome map and so on. More features: visualization of sequence logos, sequence bundles, RNA secondary structures and detection of sequence recombinations.

package bioconductor-ggmsa¶

Versions:

1.16.0-0, 1.12.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-0, 1.0.0-0

Depends:

on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-ggtree >=4.0.0,<4.1.0
on bioconductor-r4rna >=1.38.0,<1.39.0
on r-aplot
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-ggforce
on r-ggfun >=0.2.0
on r-ggplot2
on r-magrittr
on r-rcolorbrewer
on r-seqmagick
on r-tidyr

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-ggmsa

to add into an existing workspace instead, run:

pixi add bioconductor-ggmsa

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-ggmsa

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-ggmsa

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-ggmsa:<tag>

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