Package: HybridExpress 1.9.0

Fabricio Almeida-Silva

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

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.

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

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HybridExpress/json (API)

# Install 'HybridExpress' in R:

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

Bug tracker:https://github.com/almeidasilvaf/hybridexpress/issues

Datasets:

deg_counts - Data frame with frequencies (absolute and relative) of DEGs per contrast
deg_list - List of differentially expressed genes for all contrasts
go_chlamy - Data frame with GO terms annotated to each gene of Chlamydomonas reinhardtii
se_chlamy - Expression data

On BioConductor:HybridExpress-1.9.0(bioc 3.24)HybridExpress-1.8.0(bioc 3.23)

software functionalgenomics geneexpression transcriptomics rnaseq classification differentialexpression gene-expression hybrid polyploidy rna-seq

5.23 score 17 stars 4 scripts 11 exports 62 dependencies

Last updated from:43455b3891. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	196
linux-devel-x86_64	OK	382
source / vignettes	OK	304
linux-release-x86_64	OK	350
macos-release-arm64	OK	254
macos-oldrel-arm64	OK	198
windows-devel	OK	276
windows-release	OK	262
windows-oldrel	OK	253
wasm-release	OK	189

Exports:add_midparent_expression add_size_factors expression_partitioning get_deg_counts get_deg_list ora pca_plot plot_expression_partitions plot_expression_triangle plot_partition_frequencies plot_samplecor

Dependencies:abind BH Biobase BiocGenerics BiocParallel circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon DelayedArray DESeq2 digest doParallel farver foreach formatR futile.logger futile.options generics GenomicRanges GetoptLong ggplot2 GlobalOptions glue gtable IRanges isoband iterators labeling lambda.r lattice lifecycle locfit Matrix MatrixGenerics matrixStats patchwork png R6 RColorBrewer Rcpp RcppArmadillo rjson rlang S4Arrays S4Vectors S7 scales Seqinfo shape snow SparseArray SummarizedExperiment vctrs viridisLite withr XVector

Comparative transcriptomic analysis of hybrids and their progenitors

Rendered fromHybridExpress.Rmdusingknitr::rmarkdown

Last update: 2024-02-23
Started: 2023-10-17

Help page	Topics
Add midparent expression to 'SummarizedExperiment' object	add_midparent_expression
Add size factors to normalize count data by library size or by biomass	add_size_factors
Data frame with frequencies (absolute and relative) of DEGs per contrast	deg_counts
List of differentially expressed genes for all contrasts	deg_list
Partition genes in groups based on their expression patterns	expression_partitioning
Get a count table of differentially expressed genes per contrast	get_deg_counts
Get a table of differential expression expression statistics with DESeq2	get_deg_list
Data frame with GO terms annotated to each gene of Chlamydomonas reinhardtii	go_chlamy
Perform overrepresentation analysis for a set of genes	ora
Perform a principal component analysis (PCA) and plot PCs	pca_plot
Plot expression partitions	plot_expression_partitions
Plot a triangle of comparisons of DEG sets among generations	plot_expression_triangle
Plot a barplot of gene frequencies per expression partition	plot_partition_frequencies
Plot a heatmap of pairwise sample correlations with hierarchical clustering	plot_samplecor
Expression data (in counts) for 3 Chlamydomonas lines (P1, P2, and F1)	se_chlamy

Package: HybridExpress 1.9.0

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

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