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Bioconductor - DifferentialRegulation (development version)

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 (3.22)

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: 0000-0002-3054-9964 , Charlotte Soneson [aut] ORCID: 0000-0003-3833-2169

Maintainer: Simone Tiberi <simone.tiberi at unibo.it>

Citation (from within R, enter 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")

Details biocViews Bayesian, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneTarget, Genetics, MultipleComparison, RNASeq, Sequencing, SingleCell, Software, StatisticalMethod, Transcription, Visualization Version 2.7.0 In Bioconductor since BioC 3.15 (R-4.2) (3 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 Package Archives

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

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