M3Drop

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Bioconductor version: 3.23 · Package version: 1.38.0

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	RELEASE_3_23
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_1.38.0.tar.gz
Windows binary (x86_64)	M3Drop_1.38.0.zip
macOS binary (arm64)	M3Drop_1.38.0.tgz
macOS binary (x86_64)	M3Drop_1.38.0.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