recipe bioconductor-vdjdive

Analysis Tools for 10X V(D)J Data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/VDJdive.html

License:

Artistic-2.0

Recipe:

/bioconductor-vdjdive/meta.yaml

This package provides functions for handling and analyzing immune receptor repertoire data, such as produced by the CellRanger V(D)J pipeline. This includes reading the data into R, merging it with paired single-cell data, quantifying clonotype abundances, calculating diversity metrics, and producing common plots. It implements the E-M Algorithm for clonotype assignment, along with other methods, which makes use of ambiguous cells for improved quantification.

package bioconductor-vdjdive

versions:

1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0a0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0a0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0a0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0a0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-cowplot:

depends r-ggplot2:

depends r-gridextra:

depends r-matrix:

depends r-rcolorbrewer:

depends r-rcpp:

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-vdjdive

and update with::

   mamba update bioconductor-vdjdive

To create a new environment, run:

mamba create --name myenvname bioconductor-vdjdive

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-vdjdive:<tag>

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

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