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README.md

zinbwave

Zero-inflated Negative Binomial based Wanted Variation Extraction (ZINB-WaVE)

Project Status: Active - The project has reached a stable, usable state and is being actively developed. Build Status Coverage

This package implements a zero-inflated negative binomial model for single-cell RNA-seq data, with latent factors.

The model is described in details in the paper:

D. Risso, F. Perraudeau, S. Gribkova, S. Dudoit and JP. Vert (2018). A general and flexible method for signal extraction from single-cell RNA-seq data. Nature Communications.

Installation

Since Bioconductor 3.7 the new recommended way to install Bioconductor packages is via the BiocManager package, available on CRAN:

install.packages("BiocManager")
BiocManager::install("zinbwave")

Note that zinbwave requires R (>=3.4) and Bioconductor (>=3.6).

In virtually all cases, installing from Bioconductor is recommended. However, if you want to install the development version of zinbwave from GitHub, you can do so with the following.

library(devtools)
install_github("drisso/zinbwave")