HybridExpress
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see HybridExpress.
Comparative analysis of RNA-seq data for hybrids and their progenitors
Bioconductor version: 3.19
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("HybridExpress")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text |
Details
| biocViews | Classification, DifferentialExpression, FunctionalGenomics, GeneExpression, RNASeq, Software, Transcriptomics |
| Version | 1.0.1 |
| 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) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HybridExpress_1.0.1.tar.gz |
| Windows Binary (x86_64) | HybridExpress_1.0.1.zip |
| macOS Binary (x86_64) | HybridExpress_1.0.1.tgz |
| macOS Binary (arm64) | HybridExpress_1.0.1.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 |
| Old Source Packages for BioC 3.19 | Source Archive |