DifferentialRegulation
This is the development version of DifferentialRegulation; for the stable release version, see DifferentialRegulation.
Differentially regulated genes from scRNA-seq data
Bioconductor version: Development (3.21)
DifferentialRegulation is a method for detecting differentially regulated genes between two groups of samples (e.g., healthy vs. disease, or treated vs. untreated samples), by targeting differences in the balance of spliced and unspliced mRNA abundances, obtained from single-cell RNA-sequencing (scRNA-seq) data. From a mathematical point of view, DifferentialRegulation accounts for the sample-to-sample variability, and embeds multiple samples in a Bayesian hierarchical model. Furthermore, our method also deals with two major sources of mapping uncertainty: i) 'ambiguous' reads, compatible with both spliced and unspliced versions of a gene, and ii) reads mapping to multiple genes. In particular, ambiguous reads are treated separately from spliced and unsplced reads, while reads that are compatible with multiple genes are allocated to the gene of origin. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques (Metropolis-within-Gibbs).
Author: Simone Tiberi [aut, cre] (ORCID:
Maintainer: Simone Tiberi <simone.tiberi at unibo.it>
citation("DifferentialRegulation")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("DifferentialRegulation")
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("DifferentialRegulation")| DifferentialRegulation | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneTarget, Genetics, MultipleComparison, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod, Transcription, Visualization |
| Version | 2.5.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.3.0) |
| Imports | methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, Matrix, SingleCellExperiment, SummarizedExperiment, ggplot2, tximport, gridExtra |
| System Requirements | C++17 |
| URL | https://github.com/SimoneTiberi/DifferentialRegulation |
| Bug Reports | https://github.com/SimoneTiberi/DifferentialRegulation/issues |
See More
| Suggests | knitr, rmarkdown, testthat, BiocStyle |
| Linking To | Rcpp, RcppArmadillo |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DifferentialRegulation_2.5.0.tar.gz |
| Windows Binary (x86_64) | DifferentialRegulation_2.5.0.zip |
| macOS Binary (x86_64) | DifferentialRegulation_2.5.0.tgz |
| macOS Binary (arm64) | DifferentialRegulation_2.5.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DifferentialRegulation |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DifferentialRegulation |
| Bioc Package Browser | https://code.bioconductor.org/browse/DifferentialRegulation/ |
| Package Short Url | https://bioconductor.org/packages/DifferentialRegulation/ |
| Package Downloads Report | Download Stats |