recipe bioconductor-phyloprofile

PhyloProfile

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/PhyloProfile.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-phyloprofile/meta.yaml

PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.

package bioconductor-phyloprofile

versions:

1.16.0-0,  1.14.5-0,  1.12.0-0,  1.8.0-0,  1.6.1-0,  1.4.9-0,  1.4.0-0,  1.2.8-1,  1.2.6-0, 

1.16.0-0,  1.14.5-0,  1.12.0-0,  1.8.0-0,  1.6.1-0,  1.4.9-0,  1.4.0-0,  1.2.8-1,  1.2.6-0,  1.2.5-0,  1.2.2-0,  1.0.1-0

depends bioconductor-biocstyle:

>=2.30.0,<2.31.0

depends bioconductor-biodist:

>=1.74.0,<1.75.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-experimenthub:

>=2.10.0,<2.11.0

depends bioconductor-omadb:

>=2.18.0,<2.19.0

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-colourpicker:

depends r-data.table:

depends r-dt:

depends r-energy:

depends r-ggplot2:

depends r-gridextra:

depends r-pbapply:

depends r-plyr:

depends r-rcolorbrewer:

depends r-rcurl:

depends r-shiny:

depends r-shinybs:

depends r-shinycssloaders:

depends r-shinyfiles:

depends r-shinyjs:

depends r-stringr:

depends r-xml2:

depends r-yaml:

depends r-zoo:

requirements:

additional platforms:

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-phyloprofile

and update with::

   mamba update bioconductor-phyloprofile

To create a new environment, run:

mamba create --name myenvname bioconductor-phyloprofile

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-phyloprofile:<tag>

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

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-phyloprofile/README.html)