M3Drop
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Bioconductor version: Release (3.20)
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 | 1.32.0 |
| 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_1.32.0.tar.gz |
| Windows Binary (x86_64) | M3Drop_1.32.0.zip |
| macOS Binary (x86_64) | M3Drop_1.32.0.tgz |
| macOS Binary (arm64) | M3Drop_1.32.0.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 |