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NewWave

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

Negative binomial model for scRNA-seq


Bioconductor version: Development (3.20)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("NewWave")

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

Documentation

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

browseVignettes("NewWave")
vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, Coverage, GeneExpression, Regression, Sequencing, SingleCell, Software, Transcriptomics
Version 1.15.0
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
URL
Bug Reports https://github.com/fedeago/NewWave/issues
See More
Suggests testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package NewWave_1.15.0.tar.gz
Windows Binary NewWave_1.15.0.zip (64-bit only)
macOS Binary (x86_64) NewWave_1.15.0.tgz
macOS Binary (arm64) NewWave_1.15.0.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