zinbwave

DOI: 10.18129/B9.bioc.zinbwave    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see zinbwave.

Zero-Inflated Negative Binomial Model for RNA-Seq Data

Bioconductor version: 3.7

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>

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("zinbwave")

 

HTML	R Script	zinbwave Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	DimensionReduction, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.2.0
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, DESeq2, Seurat
SystemRequirements
Enhances
URL
BugReports	https://github.com/drisso/zinbwave/issues
Depends On Me
Imports Me
Suggests Me	splatter
Links To Me
Build Report

Package Archives

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

Source Package	zinbwave_1.2.0.tar.gz
Windows Binary	zinbwave_1.2.0.zip
Mac OS X 10.11 (El Capitan)	zinbwave_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/zinbwave
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/zinbwave
Package Short Url	http://bioconductor.org/packages/zinbwave/
Package Downloads Report	Download Stats