Package Recipe 'bioconductor-phyloprofile'

recipe bioconductor-phyloprofile

PhyloProfile

Homepage:: https://bioconductor.org/packages/3.20/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:

2.2.2-0, 1.20.0-0, 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,

2.2.2-0, 1.20.0-0, 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:

on bioconductor-biocstyle >=2.38.0,<2.39.0
on bioconductor-biodist >=1.82.0,<1.83.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on r-ape
on r-base >=4.5,<4.6.0a0
on r-bsplus
on r-colourpicker
on r-data.table
on r-dplyr
on r-dt
on r-energy
on r-fastcluster
on r-ggplot2
on r-gridextra
on r-htmlwidgets
on r-pbapply
on r-plotly
on r-rcolorbrewer
on r-rcurl
on r-rfast
on r-scattermore
on r-shiny
on r-shinycssloaders
on r-shinyfiles
on r-shinyjs
on r-stringr
on r-svglite
on r-tsne
on r-umap
on r-xml2
on r-yaml
on r-zoo

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-phyloprofile

to add into an existing workspace instead, run:

pixi add bioconductor-phyloprofile

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-phyloprofile

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-phyloprofile

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-phyloprofile:<tag>

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