NewWave

DOI: 10.18129/B9.bioc.NewWave    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see NewWave.

Negative binomial model for scRNA-seq

Bioconductor version: 3.15

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>

Installation

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

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

browseVignettes("NewWave")

 

HTML	R Script	vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, Coverage, GeneExpression, Regression, Sequencing, SingleCell, Software, Transcriptomics
Version	1.6.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 years)
License	GPL-3
Depends	R (>= 4.0), SummarizedExperiment
Imports	methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, SharedObject, stats
LinkingTo
Suggests	testthat, rmarkdown, splatter, mclust, Rtsne, ggplot2, Rcpp, BiocStyle, knitr
SystemRequirements
Enhances
URL
BugReports	https://github.com/fedeago/NewWave/issues
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_1.6.0.tar.gz
Windows Binary	NewWave_1.6.0.zip
macOS Binary (x86_64)	NewWave_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/NewWave
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NewWave
Package Short Url	https://bioconductor.org/packages/NewWave/
Package Downloads Report	Download Stats