Package Recipe 'bioconductor-cellarepertorium'

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:

on bioconductor-biocgenerics >=0.48.0,<0.49.0
on bioconductor-biocgenerics >=0.48.1,<0.49.0a0
on bioconductor-biostrings >=2.70.0,<2.71.0
on bioconductor-biostrings >=2.70.1,<2.71.0a0
on bioconductor-s4vectors >=0.40.0,<0.41.0
on bioconductor-s4vectors >=0.40.2,<0.41.0a0
on libblas >=3.9.0,<4.0a0
on libgcc-ng >=12
on liblapack >=3.9.0,<4.0a0
on libstdcxx-ng >=12
on r-base >=4.3,<4.4.0a0
on r-dplyr
on r-forcats
on r-generics
on r-glue
on r-matrix
on r-progress
on r-purrr
on r-rcpp
on r-reshape2
on r-rlang >=0.3
on r-stringr
on r-tibble
on r-tidyr

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-cellarepertorium

to add into an existing workspace instead, run:

pixi add bioconductor-cellarepertorium

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-cellarepertorium

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cellarepertorium

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-cellarepertorium:<tag>

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