recipe bioconductor-cellarepertorium

Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-cellarepertorium/meta.yaml

Methods to cluster and analyze high-throughput single cell immune cell repertoires, especially from the 10X Genomics VDJ solution. Contains an R interface to CD-HIT (Li and Godzik 2006). Methods to visualize and analyze paired heavy-light chain data. Tests for specific expansion, as well as omnibus oligoclonality under hypergeometric models.

package bioconductor-cellarepertorium

versions:

1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.4.0-2,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-2, 

1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.4.0-2,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-2,  1.0.0-1

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biocgenerics:

>=0.48.1,<0.49.0a0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-biostrings:

>=2.70.1,<2.71.0a0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-forcats:

depends r-generics:

depends r-glue:

depends r-matrix:

depends r-progress:

depends r-purrr:

depends r-rcpp:

depends r-reshape2:

depends r-rlang:

>=0.3

depends r-stringr:

depends r-tibble:

depends r-tidyr:

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-cellarepertorium

and update with::

   mamba update bioconductor-cellarepertorium

To create a new environment, run:

mamba create --name myenvname bioconductor-cellarepertorium

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-cellarepertorium:<tag>

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

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