M3Drop

DOI: 10.18129/B9.bioc.M3Drop  

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Bioconductor version: Release (3.16)

This package fits a Michaelis-Menten 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.

Author: Tallulah Andrews <tallulandrews at gmail.com>

Maintainer: Tallulah Andrews <tallulandrews at gmail.com>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	DifferentialExpression, DimensionReduction, FeatureExtraction, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics
Version	1.24.0
In Bioconductor since	BioC 3.4 (R-3.3) (6.5 years)
License	GPL (>=2)
Depends	R (>= 3.4), numDeriv
Imports	RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods
LinkingTo
Suggests	ROCR, knitr, M3DExampleData, scater, SingleCellExperiment, monocle, Seurat, Biobase
SystemRequirements
Enhances
URL	https://github.com/tallulandrews/M3Drop
BugReports	https://github.com/tallulandrews/M3Drop/issues
Depends On Me
Imports Me	scMerge
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	M3Drop_1.24.0.tar.gz
Windows Binary	M3Drop_1.24.0.zip
macOS Binary (x86_64)	M3Drop_1.24.0.tgz
macOS Binary (arm64)	M3Drop_1.24.0.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