recipe bioconductor-abseqr

Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries

Homepage:

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

License:

GPL-3 | file LICENSE

Recipe:

/bioconductor-abseqr/meta.yaml

AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. abseqR empowers the users of abseqPy (https://github.com/malhamdoosh/abseqPy) with plotting and reporting capabilities and allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output.

package bioconductor-abseqr

versions:

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0, 

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-biocstyle:

>=2.30.0,<2.31.0

depends pandoc:

>=1.19.2.1

depends r-base:

>=4.3,<4.4.0a0

depends r-circlize:

depends r-flexdashboard:

depends r-ggcorrplot:

depends r-ggdendro:

depends r-ggplot2:

depends r-gridextra:

depends r-knitr:

depends r-plotly:

depends r-plyr:

depends r-png:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-rmarkdown:

depends r-stringr:

depends r-vegan:

depends r-venndiagram:

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-abseqr

and update with::

   mamba update bioconductor-abseqr

To create a new environment, run:

mamba create --name myenvname bioconductor-abseqr

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-abseqr:<tag>

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

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