recipe bioconductor-lineagepulse

Differential expression analysis and model fitting for single-cell RNA-seq data

Homepage

https://bioconductor.org/packages/3.11/bioc/html/LineagePulse.html

License

Artistic-2.0

Recipe

/bioconductor-lineagepulse/meta.yaml

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.

package bioconductor-lineagepulse

Versions

1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-0

Depends

• bioconductor-biocparallel >=1.22.0,<1.23.0

• bioconductor-complexheatmap >=2.4.0,<2.5.0

• bioconductor-singlecellexperiment >=1.10.0,<1.11.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• r-base >=4.0,<4.1.0a0

• r-circlize

• r-ggplot2

• r-gplots

• r-knitr

• r-matrix

• r-rcolorbrewer

Required By

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>)

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-lineagepulse/README.html)