recipe bioconductor-desingle

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

Homepage

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

License

GPL-2

Recipe

/bioconductor-desingle/meta.yaml

DEsingle is an R package for differential expression (DE) analysis of single-cell RNA-seq (scRNA-seq) data. It defines and detects 3 types of differentially expressed genes between two groups of single cells, with regard to different expression status (DEs), differential expression abundance (DEa), and general differential expression (DEg). DEsingle employs Zero-Inflated Negative Binomial model to estimate the proportion of real and dropout zeros and to define and detect the 3 types of DE genes. Results showed that DEsingle outperforms existing methods for scRNA-seq DE analysis, and can reveal different types of DE genes that are enriched in different biological functions.

package bioconductor-desingle

Versions

1.8.0-0, 1.6.0-0, 1.4.0-1, 1.4.0-0, 1.2.1-0

Depends

• bioconductor-biocparallel >=1.22.0,<1.23.0

• r-base >=4.0,<4.1.0a0

• r-bbmle >=1.0.18

• r-gamlss >=4.4-0

• r-mass >=7.3-45

• r-matrix >=1.2-14

• r-maxlik >=1.3-4

• r-pscl >=1.4.9

• r-vgam >=1.0-2

Required By

Installation

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

conda install bioconductor-desingle

and update with:

conda update bioconductor-desingle

or use the docker container:

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

(see bioconductor-desingle/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-desingle/README.html)