DOI: 10.18129/B9.bioc.NewWave  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see NewWave.

Negative binomial model for scRNA-seq

Bioconductor version: 3.16

A model designed for dimensionality reduction and batch effect removal for scRNA-seq data. It is designed to be massively parallelizable using shared objects that prevent memory duplication, and it can be used with different mini-batch approaches in order to reduce time consumption. It assumes a negative binomial distribution for the data with a dispersion parameter that can be both commonwise across gene both genewise.

Author: Federico Agostinis [aut, cre], Chiara Romualdi [aut], Gabriele Sales [aut], Davide Risso [aut]

Maintainer: Federico Agostinis <federico.agostinis at>

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


To install this package, start R (version "4.2") and enter:

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


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


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



HTML R Script vignette
PDF   Reference Manual
Text   NEWS


biocViews BatchEffect, Coverage, GeneExpression, Regression, Sequencing, SingleCell, Software, Transcriptomics
Version 1.8.0
In Bioconductor since BioC 3.12 (R-4.0) (2.5 years)
License GPL-3
Depends R (>= 4.0), SummarizedExperiment
Imports methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats
Suggests testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package NewWave_1.8.0.tar.gz
Windows Binary
macOS Binary (x86_64) NewWave_1.8.0.tgz
macOS Binary (arm64) NewWave_1.8.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: