Package: MAST Type: Package Title: Model-based Analysis of Single Cell Transcriptomics Version: 1.25.0 Date: 2021-12-15 Authors@R: c(person("Andrew", "McDavid", email = "[email protected]", role = c("aut", "cre")), person("Greg", "Finak", email="[email protected]", role='aut'), person("Masanao", "Yajima", email="[email protected]", role='aut')) VignetteBuilder: knitr Imports: Biobase, BiocGenerics, S4Vectors, data.table, ggplot2, plyr, stringr, abind, methods, parallel, reshape2, stats, stats4, graphics, utils, SummarizedExperiment(>= 1.5.3), progress Depends: SingleCellExperiment (>= 1.2.0), R(>= 3.5) Suggests: knitr, rmarkdown, testthat, lme4(>= 1.0), blme, roxygen2(> 6.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF, TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer, BiocStyle, scater, DelayedArray, Matrix, HDF5Array, zinbwave, dplyr Description: Methods and models for handling zero-inflated single cell assay data. License: GPL(>= 2) Collate: 'AllGenerics.R' 'AllClasses.R' 'CovFromBoots.R' 'Fluidigm-methods.R' 'GSEA-by-boot.R' 'Hypothesis.R' 'LmWrapper.R' 'MAST-package.R' 'MultidimensionalScaling.R' 'RNASeqAssay-methods.R' 'Readers.R' 'SingleCellAssay-methods.R' 'UtilityFunctions.R' 'ZlmFit-bootstrap.R' 'ZlmFit-logFC.R' 'ZlmFit.R' 'bayesglm.R' 'convertMASTClassic.R' 'ebayes-helpers.R' 'filterEval.R' 'helper-methods.R' 'lmWrapper-bayesglm.R' 'lmWrapper-glm.R' 'lmWrapper-glmer.R' 'lmWrapper-ridge.R' 'lrtest.R' 'predict.R' 'stat_ell.R' 'thresholdSCRNA.R' 'zeroinf.R' 'zlmHooks.R' RoxygenNote: 7.1.2 LazyData: true biocViews: GeneExpression, DifferentialExpression, GeneSetEnrichment, RNASeq, Transcriptomics, SingleCell BugReports: https://github.com/RGLab/MAST/issues URL: https://github.com/RGLab/MAST/ Encoding: UTF-8