To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("zinbwave")

In most cases, you don't need to download the package archive at all.

zinbwave

DOI: 10.18129/B9.bioc.zinbwave    

Zero-Inflated Negative Binomial Model for RNA-Seq Data

Bioconductor version: Release (3.6)

Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.

Author: Davide Risso [aut, cre, cph], Svetlana Gribkova [aut], Fanny Perraudeau [aut], Jean-Philippe Vert [aut]

Maintainer: Davide Risso <risso.davide at gmail.com>

Citation (from within R, enter citation("zinbwave")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("zinbwave")

Documentation

HTML R Script zinbwave Vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews DimensionReduction, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.0.0
License Artistic-2.0
Depends R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment
Imports copula, glmnet, BiocParallel, softImpute, stats, genefilter, edgeR
LinkingTo
Suggests knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne
SystemRequirements
Enhances
URL
BugReports https://github.com/drisso/zinbwave/issues
Depends On Me
Imports Me
Suggests Me splatter
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package zinbwave_1.0.0.tar.gz
Windows Binary zinbwave_1.0.0.zip
Mac OS X 10.11 (El Capitan) zinbwave_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/zinbwave
Package Short Url http://bioconductor.org/packages/zinbwave/
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