DifferentialRegulation

DOI: 10.18129/B9.bioc.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 (3.16)

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")

# 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")

 

HTML R Script DifferentialRegulation
PDF   Reference Manual
Text   NEWS

Details

biocViews Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneTarget, Genetics, MultipleComparison, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod, Transcription, Visualization
Version 1.1.7
In Bioconductor since BioC 3.15 (R-4.2) (< 6 months)
License GPL-3
Depends R (>= 4.2.0)
Imports methods, Rcpp, doRNG, MASS, data.table, doParallel, parallel, foreach, stats, BANDITS, Matrix, SingleCellExperiment, SummarizedExperiment, ggplot2
LinkingTo Rcpp, RcppArmadillo
Suggests knitr, rmarkdown, testthat, BiocStyle
SystemRequirements C++11
Enhances
URL https://github.com/SimoneTiberi/DifferentialRegulation
BugReports https://github.com/SimoneTiberi/DifferentialRegulation/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DifferentialRegulation_1.1.7.tar.gz
Windows Binary DifferentialRegulation_1.1.7.zip
macOS 10.13 (High Sierra) DifferentialRegulation_1.1.7.tgz
Source Repository git clone https://git.bioconductor.org/packages/DifferentialRegulation
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DifferentialRegulation
Package Short Url https://bioconductor.org/packages/DifferentialRegulation/
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