NewWave
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see NewWave.
Negative binomial model for scRNA-seq
Bioconductor version: 3.19
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("NewWave")
):
Installation
To install this package, start R (version "4.4") 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")
vignette | HTML | R Script |
Reference Manual | ||
NEWS | Text |
Details
biocViews | BatchEffect, Coverage, GeneExpression, Regression, Sequencing, SingleCell, Software, Transcriptomics |
Version | 1.14.0 |
In Bioconductor since | BioC 3.12 (R-4.0) (4 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_1.14.0.tar.gz |
Windows Binary (x86_64) | NewWave_1.14.0.zip |
macOS Binary (x86_64) | NewWave_1.14.0.tgz |
macOS Binary (arm64) | NewWave_1.14.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/NewWave |
Source Repository (Developer Access) | git clone [email protected]:packages/NewWave |
Bioc Package Browser | https://code.bioconductor.org/browse/NewWave/ |
Package Short Url | https://bioconductor.org/packages/NewWave/ |
Package Downloads Report | Download Stats |