M3Drop
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Bioconductor version: Release (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("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 | R Script | |
Reference Manual | ||
README | Text | |
NEWS | Text |
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 |
See More
Suggests | ROCR, knitr, M3DExampleData, SingleCellExperiment, Seurat, Biobase |
Linking To | |
Enhances | |
Depends On Me | |
Imports Me | scMerge |
Suggests Me | |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | M3Drop_1.30.0.tar.gz |
Windows Binary | 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/ |
Package Downloads Report | Download Stats |