zinbwave
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see zinbwave.
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Bioconductor version: 3.9
Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.
Author: Davide Risso [aut, cre, cph], Svetlana Gribkova [aut], Fanny Perraudeau [aut], Jean-Philippe Vert [aut]
Maintainer: Davide Risso <risso.davide at gmail.com>
citation("zinbwave")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("zinbwave")
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("zinbwave")| zinbwave Vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.6.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment |
| Imports | copula, glmnet, BiocParallel, softImpute, stats, genefilter, edgeR, Matrix |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/drisso/zinbwave/issues |
See More
| Suggests | knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, Seurat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | clusterExperiment |
| Suggests Me | splatter |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | zinbwave_1.6.0.tar.gz |
| Windows Binary | zinbwave_1.6.0.zip |
| Mac OS X 10.11 (El Capitan) | zinbwave_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/zinbwave |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/zinbwave |
| Bioc Package Browser | https://code.bioconductor.org/browse/zinbwave/ |
| Package Short Url | https://bioconductor.org/packages/zinbwave/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |