recipe bioconductor-screpertoire

A toolkit for single-cell immune receptor profiling

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-screpertoire/meta.yaml

scRepertoire was built to process data derived from the 10x Genomics Chromium Immune Profiling for both T-cell receptor (TCR) and immunoglobulin (Ig) enrichment workflows and subsequently interacts with the popular Seurat and SingleCellExperiment R packages. It also allows for general analysis of single-cell clonotype information without the use of expression information. The package functions as a wrapper for Startrac and powerTCR R packages.

package bioconductor-screpertoire

versions:

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-powertcr:

>=1.22.0,<1.23.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-doparallel:

depends r-dplyr:

depends r-ggalluvial:

depends r-ggplot2:

depends r-ggraph:

depends r-igraph:

depends r-plyr:

depends r-reshape2:

depends r-rlang:

depends r-seuratobject:

depends r-stringdist:

depends r-stringr:

depends r-tidygraph:

depends r-vegan:

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-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>``)

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