recipe bioconductor-lineagepulse

LineagePulse is a differential expression and expression model fitting package tailored to single-cell RNA-seq data (scRNA-seq). LineagePulse accounts for batch effects, drop-out and variable sequencing depth. One can use LineagePulse to perform longitudinal differential expression analysis across pseudotime as a continuous coordinate or between discrete groups of cells (e.g. pre-defined clusters or experimental conditions). Expression model fits can be directly extracted from LineagePulse.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/LineagePulse.html

License

Artistic-2.0

Recipe

/bioconductor-lineagepulse/meta.yaml

package bioconductor-lineagepulse

(downloads) docker_bioconductor-lineagepulse

Versions

1.2.0-0

Depends bioconductor-biocparallel

>=1.16.0,<1.17.0

Depends bioconductor-complexheatmap

>=1.20.0,<1.21.0

Depends bioconductor-singlecellexperiment

>=1.4.0,<1.5.0

Depends bioconductor-summarizedexperiment

>=1.12.0,<1.13.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-circlize

Depends r-ggplot2

Depends r-gplots

Depends r-knitr

Depends r-matrix

Depends r-rcolorbrewer

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-lineagepulse

and update with:

conda update bioconductor-lineagepulse

or use the docker container:

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

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