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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.39.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 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_1.39.0.tar.gz |
| Windows Binary (x86_64) | M3Drop_1.39.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | M3Drop_1.39.0.tgz |
| macOS Binary (sonoma-arm64) | M3Drop_1.39.0.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 |