DifferentialRegulation-package: Differentially regulated genes from scRNA-seq data

In SimoneTiberi/DifferentialRegulation: Differentially regulated genes from scRNA-seq data

Differentially regulated genes from scRNA-seq data

Description

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).

Details

The DESCRIPTION file: This package was not yet installed at build time.
Questions relative to DifferentialRegulation should be reported as a new issue at https://github.com/SimoneTiberi/DifferentialRegulatio/issues.

To access the vignettes, type: browseVignettes("DifferentialRegulation").

Index: This package was not yet installed at build time.

Author(s)

Simone Tiberi [e-mail]

SimoneTiberi/DifferentialRegulation documentation built on Aug. 22, 2024, 7:43 a.m.