zinbwave
This is the development version of zinbwave; for the stable release version, see zinbwave.
All Bioconductor versions of zinbwave
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Bioconductor version: 3.24 · Package version: 1.35.0
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"):
Davide Risso, Svetlana Gribkova, Fanny Perraudeau, Jean-Philippe Vert, Clara Bagatin. zinbwave: Zero-Inflated Negative Binomial Model for RNA-Seq Data. doi:10.18129/B9.bioc.zinbwave, R package version 1.35.0, https://bioconductor.org/packages/zinbwave.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("zinbwave")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.35.0 |
| License | Artistic-2.0 |
| Bug Reports | https://github.com/drisso/zinbwave/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.6 (R-3.4) (8 years) |
| Downloads rank | 280 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DimensionReduction, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/zinbwave/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("zinbwave")| An introduction to ZINB-WaVE | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | zinbwave_1.35.0.tar.gz |
| Windows binary (x86_64) | zinbwave_1.35.0.zip |
| macOS binary (arm64) | zinbwave_1.35.0.tgz |
| macOS binary (x86_64) | zinbwave_1.35.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/zinbwave |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/zinbwave |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment
Imports: BiocParallel, softImpute, stats, genefilter, edgeR, Matrix
Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, sparseMatrixStats
Reverse dependencies
Imports Me (4): benchdamic, clusterExperiment, scBFA, singleCellTK