Package: zinbwave Type: Package Title: Zero-Inflated Negative Binomial Model for RNA-Seq Data Version: 1.35.0 Authors@R: c(person("Davide","Risso", role=c("aut","cre", "cph"), email="risso.davide@gmail.com" ), person("Svetlana","Gribkova", role="aut", email="svetlana.gribkova@mines-paristech.fr"), person("Fanny", "Perraudeau", role="aut", email="fperraudeau@berkeley.edu"), person("Jean-Philippe", "Vert", role="aut", email="jean-philippe.vert@mines-paristech.fr"), person("Clara", "Bagatin", role="aut", email="clarabagatin@yahoo.it")) Description: 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. 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, sparseMatrixStats VignetteBuilder: knitr LazyData: TRUE RoxygenNote: 7.3.1 biocViews: ImmunoOncology, DimensionReduction, GeneExpression, RNASeq, Software, Transcriptomics, Sequencing, SingleCell BugReports: https://github.com/drisso/zinbwave/issues Config/pak/sysreqs: libpng-dev libxml2-dev libssl-dev zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 12:45:49 UTC RemoteUrl: https://github.com/bioc/zinbwave RemoteRef: HEAD RemoteSha: 6100d53205b3a7274c697bc2ea635484f070aa7f NeedsCompilation: no Packaged: 2026-07-03 17:50:04 UTC; root Author: Davide Risso [aut, cre, cph], Svetlana Gribkova [aut], Fanny Perraudeau [aut], Jean-Philippe Vert [aut], Clara Bagatin [aut] Maintainer: Davide Risso