Package: DifferentialRegulation 2.3.0

Simone Tiberi

DifferentialRegulation: Differentially regulated genes from scRNA-seq data

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).

Authors:Simone Tiberi [aut, cre], Charlotte Soneson [aut]

# Install 'DifferentialRegulation' in R:

install.packages('DifferentialRegulation', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/simonetiberi/differentialregulation/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

On BioConductor:DifferentialRegulation-2.3.0(bioc 3.20)DifferentialRegulation-2.2.0(bioc 3.19)

bioconductor-package

11 exports 0.61 score 87 dependencies

Last updated 2 months agofrom:fb49478c3c

Exports:compute_PB_counts DifferentialRegulation DifferentialRegulation_bulk load_bulk_EC load_bulk_US load_EC load_USA plot_bulk_pi plot_bulk_traceplot plot_pi plot_traceplot

Dependencies:abind askpass BANDITS BH Biobase BiocGenerics BiocParallel cli codetools colorspace cpp11 crayon curl data.table DelayedArray digest doParallel doRNG DRIMSeq edgeR fansi farver foreach formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 glue gridExtra gtable httr IRanges isoband iterators jsonlite labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig plyr R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppArmadillo reshape2 rlang rngtools S4Arrays S4Vectors scales SingleCellExperiment snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tximport UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

DifferentialRegulation: a method to identify genes displaying differential regulation between groups of samples

Simone Tiberi, Charlotte Soneson

Rendered fromDifferentialRegulation.Rmdusingknitr::rmarkdownon Jun 12 2024.

Last update: 2024-01-22
Started: 2022-04-01

Help page	Topics
Differentially regulated genes from scRNA-seq data	DifferentialRegulation-package
Discover differentially regulated genes	compute_PB_counts
Discover differentially regulated genes from single-cell RNA-seq data	DifferentialRegulation
Discover differentially regulated genes from bulk RNA-seq data	DifferentialRegulation_bulk
Create a list containing the equivalence classes objects for the bulk RNA-seq data	load_bulk_EC
Creates a SummarizedExperiment containing the estimated US counts for the bulk RNA-seq data	load_bulk_US
Create a list containing the equivalence classes objects for the single-cell RNA-seq data	load_EC
Creates a SingleCellExperiment containing the estimated USA counts for the single-cell RNA-seq data	load_USA
Plot the estimated proportions of US counts in each group - bulk RNA-seq data	plot_bulk_pi
Traceplot of the posterior chain of the proportion (i.e., pi) of unspliced (U) counts in each group - bulk RNA-seq data	plot_bulk_traceplot
Plot the estimated proportions of US or USA counts in each group - single-cell RNA-seq data	plot_pi
Traceplot of the posterior chain of the proportion (i.e., pi) of unspliced (U) counts in each group - single-cell RNA-seq data	plot_traceplot

Package: DifferentialRegulation 2.3.0

DifferentialRegulation: Differentially regulated genes from scRNA-seq data

DifferentialRegulation: a method to identify genes displaying differential regulation between groups of samples

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