DOI: 10.18129/B9.bioc.zinbwave  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see zinbwave.

Zero-Inflated Negative Binomial Model for RNA-Seq Data

Bioconductor version: 3.17

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], Clara Bagatin [aut]

Maintainer: Davide Risso <risso.davide at gmail.com>

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biocViews DimensionReduction, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.22.0
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License Artistic-2.0
Depends R (>= 3.4), methods, SummarizedExperiment, SingleCellExperiment
Imports BiocParallel, softImpute, stats, genefilter, edgeR, Matrix
Suggests knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2
BugReports https://github.com/drisso/zinbwave/issues
Depends On Me
Imports Me benchdamic, clusterExperiment, scBFA, singleCellTK
Suggests Me MAST, splatter
Links To Me
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