DifferentialRegulation

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DifferentialRegulation.

Differentially regulated genes from scRNA-seq data


Bioconductor version: 3.15

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. DifferentialRegulation accounts for the sample-to-sample variability, and embeds multiple samples in a Bayesian hierarchical model. In particular, when reads are compatible with multiple genes or multiple splicing versions of a gene (unspliced spliced or ambiguous), the method allocates these multi-mapping reads to the gene of origin and their splicing version. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques (Metropolis-within-Gibbs).

Author: Simone Tiberi [aut, cre]

Maintainer: Simone Tiberi <simone.tiberi at uzh.ch>

Citation (from within R, enter citation("DifferentialRegulation")):

Installation

To install this package, start R (version "4.2") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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 PDF
NEWS Text

Details

biocViews Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneTarget, Genetics, MultipleComparison, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod, Transcription, Visualization
Version 1.0.7
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends R (>= 4.2.0)
Imports methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, Matrix, SingleCellExperiment, SummarizedExperiment, ggplot2
System Requirements C++11
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_1.0.7.tar.gz
Windows Binary DifferentialRegulation_1.0.7.zip
macOS Binary (x86_64) DifferentialRegulation_1.0.7.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
Old Source Packages for BioC 3.15 Source Archive