Package Recipe 'bioconductor-pfamanalyzer'

recipe bioconductor-pfamanalyzer

Identification of domain isotypes in pfam data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/pfamAnalyzeR.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-pfamanalyzer/meta.yaml

Protein domains is one of the most import annoation of proteins we have with the Pfam database/tool being (by far) the most used tool. This R package enables the user to read the pfam prediction from both webserver and stand-alone runs into R. We have recently shown most human protein domains exist as multiple distinct variants termed domain isotypes. Different domain isotypes are used in a cell, tissue, and disease-specific manner. Accordingly, we find that domain isotypes, compared to each other, modulate, or abolish the functionality of a protein domain. This R package enables the identification and classification of such domain isotypes from Pfam data.

package bioconductor-pfamanalyzer¶

Versions:

1.10.0-0, 1.6.0-0, 1.2.0-0, 1.0.1-0

Depends:

on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-magrittr
on r-readr
on r-stringr
on r-tibble

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-pfamanalyzer

to add into an existing workspace instead, run:

pixi add bioconductor-pfamanalyzer

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-pfamanalyzer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-pfamanalyzer

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-pfamanalyzer:<tag>

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