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 (3.21)

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] (ORCID: ), Lucas Prost-Boxoen [aut] (ORCID: ), Yves Van de Peer [aut] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, DifferentialExpression, FunctionalGenomics, GeneExpression, RNASeq, Software, Transcriptomics
Version	1.3.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
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

Suggests	BiocStyle, knitr, sessioninfo, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
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Build Report	Build Report

Package Archives

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

Source Package	HybridExpress_1.3.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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