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NewWave

Negative binomial model for scRNA-seq

Bioconductor version: Release (3.17)

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")):

Installation

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

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

BiocManager::install("NewWave")

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

Documentation

Reference Manual PDF

Details

biocViews BatchEffect, Coverage, GeneExpression, Regression, Sequencing, SingleCell, Software, Transcriptomics
Version 1.10.0
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License GPL-3
Depends R (>= 4.0), SummarizedExperiment
Imports methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats
Linking To
Suggests testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr
System Requirements
Enhances
URL
Bug Reports https://github.com/fedeago/NewWave/issues
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Build Report  

Package Archives

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

Source Package
Windows Binary NewWave_1.10.0.zip
macOS Binary (x86_64) NewWave_1.10.0.tgz
macOS Binary (arm64) NewWave_1.10.0.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/
Package Downloads Report Download Stats