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Zero-Inflated Negative Binomial Model for RNA-Seq Data

Bioconductor version: Release (3.18)

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], Clara Bagatin [aut]

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

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


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


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


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Reference Manual PDF


biocViews DimensionReduction, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.24.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License Artistic-2.0
Depends R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment
Imports BiocParallel, softImpute, stats, genefilter, edgeR, Matrix
System Requirements
Bug Reports https://github.com/drisso/zinbwave/issues
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Suggests knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2
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Depends On Me
Imports Me benchdamic, clusterExperiment, scBFA, singleCellTK
Suggests Me MAST, splatter
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Follow Installation instructions to use this package in your R session.

Source Package zinbwave_1.24.0.tar.gz
Windows Binary zinbwave_1.24.0.zip (64-bit only)
macOS Binary (x86_64) zinbwave_1.24.0.tgz
macOS Binary (arm64) zinbwave_1.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/zinbwave
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/zinbwave
Bioc Package Browser https://code.bioconductor.org/browse/zinbwave/
Package Short Url https://bioconductor.org/packages/zinbwave/
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