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This is the development version of NewWave; for the stable release version, see NewWave.

Negative binomial model for scRNA-seq

Bioconductor version: Development (3.19)

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 outlook.com>

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


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biocViews BatchEffect, Coverage, GeneExpression, Regression, Sequencing, SingleCell, Software, Transcriptomics
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.0), SummarizedExperiment
Imports methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats
System Requirements
Bug Reports https://github.com/fedeago/NewWave/issues
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Suggests testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr
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Source Package NewWave_1.13.0.tar.gz
Windows Binary NewWave_1.13.0.zip
macOS Binary (x86_64) NewWave_1.13.0.tgz
macOS Binary (arm64) NewWave_1.13.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/NewWave
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NewWave
Bioc Package Browser https://code.bioconductor.org/browse/NewWave/
Package Short Url https://bioconductor.org/packages/NewWave/
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