recipe bioconductor-screpertoire

A toolkit for single-cell immune receptor profiling

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-screpertoire/meta.yaml

scRepertoire is a toolkit for processing and analyzing single-cell T-cell receptor (TCR) and immunoglobulin (Ig). The scRepertoire framework supports use of 10x, AIRR, BD, MiXCR, Omniscope, TRUST4, and WAT3R single-cell formats. The functionality includes basic clonal analyses, repertoire summaries, distance-based clustering and interaction with the popular Seurat and SingleCellExperiment/Bioconductor R workflows.

package bioconductor-screpertoire

versions:

2.2.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

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-cubature:

depends r-dplyr:

depends r-evmix:

depends r-ggalluvial:

depends r-ggdendro:

depends r-ggplot2:

depends r-ggraph:

depends r-hash:

depends r-igraph:

depends r-inext:

depends r-plyr:

depends r-quantreg:

depends r-rcpp:

depends r-reshape2:

depends r-rjson:

depends r-rlang:

depends r-seuratobject:

depends r-stringdist:

depends r-stringr:

depends r-tidygraph:

depends r-truncdist:

depends r-vgam:

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-screpertoire

and update with::

   mamba update bioconductor-screpertoire

To create a new environment, run:

mamba create --name myenvname bioconductor-screpertoire

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-screpertoire:<tag>

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

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-screpertoire/README.html)