M3Drop

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see M3Drop.

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Bioconductor version: 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

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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/

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