recipe bioconductor-vdjdive

Analysis Tools for 10X V(D)J Data

Homepage:

https://bioconductor.org/packages/3.16/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:

1.0.0-0

Depends:

• bioconductor-basilisk >=1.9.0,<1.10.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-singlecellexperiment >=1.20.0,<1.21.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• r-base >=4.2,<4.3.0a0

• r-cowplot

• r-ggplot2

• r-gridextra

• r-matrix

• r-rcolorbrewer

• r-reticulate

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-vdjdive

and update with:

conda update bioconductor-vdjdive

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-vdjdive:<tag>

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

Download stats

Link to this page

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