HybridExpress

This is the development version of HybridExpress; for the stable release version, see HybridExpress.

Comparative analysis of RNA-seq data for hybrids and their progenitors


Bioconductor version: Development (3.20)

HybridExpress can be used to perform comparative transcriptomics analysis of hybrids (or allopolyploids) relative to their progenitor species. The package features functions to perform exploratory analyses of sample grouping, identify differentially expressed genes in hybrids relative to their progenitors, classify genes in expression categories (N = 12) and classes (N = 5), and perform functional analyses. We also provide users with graphical functions for the seamless creation of publication-ready figures that are commonly used in the literature.

Author: Fabricio Almeida-Silva [aut, cre] , Lucas Prost-Boxoen [aut] , Yves Van de Peer [aut]

Maintainer: Fabricio Almeida-Silva <fabricio_almeidasilva at hotmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("HybridExpress")

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("HybridExpress")
Comparative transcriptomic analysis of hybrids and their progenitors HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, DifferentialExpression, FunctionalGenomics, GeneExpression, RNASeq, Software, Transcriptomics
Version 1.1.1
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL-3
Depends R (>= 4.3.0)
Imports ggplot2, patchwork, rlang, DESeq2, SummarizedExperiment, stats, methods, RColorBrewer, ComplexHeatmap, grDevices, BiocParallel
System Requirements
URL https://github.com/almeidasilvaf/HybridExpress
Bug Reports https://support.bioconductor.org/tag/HybridExpress
See More
Suggests BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0)
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Package Archives

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

Source Package HybridExpress_1.1.1.tar.gz
Windows Binary (x86_64) HybridExpress_1.1.1.zip (64-bit only)
macOS Binary (x86_64) HybridExpress_1.1.1.tgz
macOS Binary (arm64) HybridExpress_1.1.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/HybridExpress
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HybridExpress
Bioc Package Browser https://code.bioconductor.org/browse/HybridExpress/
Package Short Url https://bioconductor.org/packages/HybridExpress/
Package Downloads Report Download Stats