M3Drop

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Bioconductor version: 3.24 · Package version: 1.39.0

This package fits a model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells. Also includes an method for calculating exact Pearson residuals in UMI-tagged data using a library-size aware negative binomial model.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("M3Drop")

Details

Maintainer	Tallulah Andrews <tallulandrews@gmail.com>
Author	Tallulah Andrews <tallulandrews@gmail.com>
License	GPL (>=2)
URL	https://github.com/tallulandrews/M3Drop
Bug Reports	https://github.com/tallulandrews/M3Drop/issues
Downloads rank	739
Source branch	devel
biocViews	DifferentialExpression, DimensionReduction, FeatureExtraction, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics

Documentation

Introduction to M3Drop

Download

Follow the installation instructions to use this package in your R session.

Source package	M3Drop_1.39.0.tar.gz
Windows binary (x86_64)	M3Drop_1.39.0.zip
macOS binary (arm64)	M3Drop_1.39.0.tgz
macOS binary (x86_64)	M3Drop_1.39.0.tgz

Dependencies

Depends: R (>= 3.4), numDeriv

Imports: RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods, scater

Suggests: ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat, Biobase

Reverse dependencies

Imports Me (1): scMerge