NewWave

DOI: 10.18129/B9.bioc.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>

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

PDF		Reference Manual

Details

biocViews	BatchEffect, Coverage, GeneExpression, Regression, Sequencing, SingleCell, Software, Transcriptomics
Version	1.10.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 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
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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