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M3Drop

This is the development version of M3Drop; for the stable release version, see M3Drop.

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq


Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("M3Drop")

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

Documentation

Reference Manual PDF

Details

biocViews DifferentialExpression, DimensionReduction, FeatureExtraction, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics
Version 1.29.7
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, scater
System Requirements
URL https://github.com/tallulandrews/M3Drop
Bug Reports https://github.com/tallulandrews/M3Drop/issues
See More
Suggests ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat, Biobase
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/M3Drop
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/M3Drop
Package Short Url https://bioconductor.org/packages/M3Drop/
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