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