Package: HybridExpress 1.8.0

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]

HybridExpress_1.8.0.tar.gz
HybridExpress_1.8.0.zip(r-4.7)HybridExpress_1.8.0.zip(r-4.6)HybridExpress_1.8.0.zip(r-4.5)
HybridExpress_1.8.0.tgz(r-4.6-any)HybridExpress_1.8.0.tgz(r-4.5-any)
HybridExpress_1.8.0.tar.gz(r-4.7-any)HybridExpress_1.8.0.tar.gz(r-4.6-any)
HybridExpress_1.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
HybridExpress/json (API)
NEWS

# Install 'HybridExpress' in R:
install.packages('HybridExpress', repos = c('https://bioc-release.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)

softwarefunctionalgenomicsgeneexpressiontranscriptomicsrnaseqclassificationdifferentialexpressiongene-expressionhybridpolyploidyrna-seq

5.20 score 16 stars 4 scripts 266 downloads 11 exports 62 dependencies

Last updated from:7969105a31 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE184
linux-devel-x86_64OK378
source / vignettesOK320
linux-release-x86_64OK386
macos-release-arm64OK244
macos-oldrel-arm64OK184
windows-develOK280
windows-releaseOK265
windows-oldrelOK249
wasm-releaseOK138

Exports:add_midparent_expressionadd_size_factorsexpression_partitioningget_deg_countsget_deg_listorapca_plotplot_expression_partitionsplot_expression_triangleplot_partition_frequenciesplot_samplecor

Dependencies:abindBHBiobaseBiocGenericsBiocParallelcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayonDelayedArrayDESeq2digestdoParallelfarverforeachformatRfutile.loggerfutile.optionsgenericsGenomicRangesGetoptLongggplot2GlobalOptionsgluegtableIRangesisobanditeratorslabelinglambda.rlatticelifecyclelocfitMatrixMatrixGenericsmatrixStatspatchworkpngR6RColorBrewerRcppRcppArmadillorjsonrlangS4ArraysS4VectorsS7scalesSeqinfoshapesnowSparseArraySummarizedExperimentvctrsviridisLitewithrXVector

Comparative transcriptomic analysis of hybrids and their progenitors

Fabricio Almeida-Silva, Lucas Prost-Boxoen, Yves Van de Peer

Rendered fromHybridExpress.Rmdusingknitr::rmarkdownon May 24 2026.

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