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Bioconductor - M3Drop

M3Drop

This is the released version of M3Drop; for the devel version, see M3Drop.

Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Bioconductor version: Release (3.21)

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 "4.5") 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")
Details biocViews DifferentialExpression, DimensionReduction, FeatureExtraction, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics Version 1.34.0 In Bioconductor since BioC 3.4 (R-3.3) (8.5 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 Package Archives

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

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