recipe bioconductor-ggmsa

Plot Multiple Sequence Alignment using 'ggplot2'

Homepage:

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

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-ggtree:

>=3.10.0,<3.11.0

depends bioconductor-r4rna:

>=1.30.0,<1.31.0

depends r-aplot:

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggalt:

depends r-ggforce:

depends r-ggplot2:

depends r-magrittr:

depends r-rcolorbrewer:

depends r-seqmagick:

depends r-statebins:

depends r-tidyr:

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-ggmsa

and update with::

   mamba update bioconductor-ggmsa

To create a new environment, run:

mamba create --name myenvname bioconductor-ggmsa

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-ggmsa:<tag>

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

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Link to this page

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