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M3Drop

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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

Details

biocViews DifferentialExpression, DimensionReduction, FeatureExtraction, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics
Version 1.28.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL (>=2)
Depends R (>= 3.4), numDeriv
Imports RColorBrewer, gplots, bbmle, statmod, grDevices, graphics, stats, matrixStats, Matrix, irlba, reldist, Hmisc, methods
System Requirements
URL https://github.com/tallulandrews/M3Drop
Bug Reports https://github.com/tallulandrews/M3Drop/issues
See More
Suggests ROCR, knitr, M3DExampleData, scater, SingleCellExperiment, monocle, Seurat, Biobase
Linking To
Enhances
Depends On Me
Imports Me scMerge
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Build Report Build Report

Package Archives

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

Source Package M3Drop_1.28.0.tar.gz
Windows Binary M3Drop_1.28.0.zip
macOS Binary (x86_64) M3Drop_1.28.0.tgz
macOS Binary (arm64) M3Drop_1.28.0.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