NewWave

DOI: 10.18129/B9.bioc.NewWave    

Negative binomial model for scRNA-seq

Bioconductor version: Release (3.12)

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 "4.0") and enter:

if (!requireNamespace("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 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License GPL-3
Depends R (>= 4.0), SummarizedExperiment, SharedObject(>= 1.3.15)
Imports methods, SingleCellExperiment, parallel, irlba, Matrix, DelayedArray, BiocSingular, 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_1.0.0.tar.gz
Windows Binary NewWave_1.0.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra) NewWave_1.0.1.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
Old Source Packages for BioC 3.12 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

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