M3Drop

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Bioconductor version: Release (3.19)

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.

Author: Tallulah Andrews <tallulandrews at gmail.com>

Maintainer: Tallulah Andrews <tallulandrews at gmail.com>

Citation (from within R, enter citation("M3Drop")):

Installation

To install this package, start R (version "4.4") and enter:


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

BiocManager::install("M3Drop")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("M3Drop")

Introduction to M3Drop	PDF	R Script
Reference Manual	PDF
README	Text
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, DimensionReduction, FeatureExtraction, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics
Version	1.30.0
In Bioconductor since	BioC 3.4 (R-3.3) (8 years)
License	GPL (>=2)
Depends	R (>= 3.4), numDeriv
Imports	RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods, scater
System Requirements
URL	https://github.com/tallulandrews/M3Drop
Bug Reports	https://github.com/tallulandrews/M3Drop/issues

Suggests	ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat, Biobase
Linking To
Enhances
Depends On Me
Imports Me	scMerge
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	M3Drop_1.30.0.tar.gz
Windows Binary (x86_64)	M3Drop_1.30.0.zip
macOS Binary (x86_64)	M3Drop_1.30.0.tgz
macOS Binary (arm64)	M3Drop_1.30.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/M3Drop
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/M3Drop
Bioc Package Browser	https://code.bioconductor.org/browse/M3Drop/
Package Short Url	https://bioconductor.org/packages/M3Drop/
Package Downloads Report	Download Stats