NewWave
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see NewWave.
Negative binomial model for scRNA-seq
Bioconductor version: 3.13
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 "4.1") 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 | 1.2.0 |
| 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_1.2.0.tar.gz |
| Windows Binary | NewWave_1.2.0.zip |
| macOS 10.13 (High Sierra) | NewWave_1.2.0.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 |
| Old Source Packages for BioC 3.13 | Source Archive |