Package: HybridExpress 1.3.0

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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NEWS

# 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-1.3.0(bioc 3.21)HybridExpress-1.2.0(bioc 3.20)

softwarefunctionalgenomicsgeneexpressiontranscriptomicsrnaseqclassificationdifferentialexpressiongene-expressionhybridpolyploidyrna-seq

5.32 score 14 stars 2 scripts 174 downloads 11 exports 80 dependencies

Last updated 5 months agofrom:7c5952c5f1. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 20 2025
R-4.5-winOKMar 20 2025
R-4.5-macOKMar 20 2025
R-4.5-linuxOKMar 20 2025
R-4.4-winOKMar 20 2025
R-4.4-macOKMar 20 2025
R-4.4-linuxOKMar 20 2025
R-4.3-winOKMar 20 2025
R-4.3-macOKMar 20 2025

Exports:add_midparent_expressionadd_size_factorsexpression_partitioningget_deg_countsget_deg_listorapca_plotplot_expression_partitionsplot_expression_triangleplot_partition_frequenciesplot_samplecor

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDelayedArrayDESeq2digestdoParallelfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigpngR6RColorBrewerRcppRcppArmadillorjsonrlangS4ArraysS4VectorsscalesshapesnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVector

Comparative transcriptomic analysis of hybrids and their progenitors

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

Rendered fromHybridExpress.Rmdusingknitr::rmarkdownon Mar 20 2025.

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