zinbwave

DOI: 10.18129/B9.bioc.zinbwave    

This is the development version of zinbwave; to use it, please install the devel version of Bioconductor.

Zero-Inflated Negative Binomial Model for RNA-Seq Data

Bioconductor version: Development (3.10)

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 (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("zinbwave")

For older versions of R, please refer to the appropriate Bioconductor release.

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

Details

biocViews DimensionReduction, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.7.1
In Bioconductor since BioC 3.6 (R-3.4) (1.5 years)
License Artistic-2.0
Depends R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment
Imports BiocParallel, softImpute, stats, genefilter, edgeR, Matrix
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 clusterExperiment
Suggests Me splatter
Links To Me
Build Report  

Package Archives

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

Source Package zinbwave_1.7.1.tar.gz
Windows Binary zinbwave_1.7.1.zip
Mac OS X 10.11 (El Capitan) zinbwave_1.7.1.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

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