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'))

Peer review:

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

5.73 score 12 stars 2 scripts 179 downloads 11 exports 81 dependencies

Last updated 2 months agofrom:7c5952c5f1. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winOKNov 20 2024
R-4.5-linuxOKNov 20 2024
R-4.4-winOKNov 20 2024
R-4.4-macOKNov 20 2024
R-4.3-winOKNov 20 2024
R-4.3-macOKNov 20 2024

Exports:add_midparent_expressionadd_size_factorsexpression_partitioningget_deg_countsget_deg_listorapca_plotplot_expression_partitionsplot_expression_triangleplot_partition_frequenciesplot_samplecor

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelcirclizecliclueclustercodetoolscolorspaceComplexHeatmapcpp11crayoncurlDelayedArrayDESeq2digestdoParallelfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2GlobalOptionsgluegtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpatchworkpillarpkgconfigpngR6RColorBrewerRcppRcppArmadillorjsonrlangS4ArraysS4VectorsscalesshapesnowSparseArraySummarizedExperimentsystibbleUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Comparative transcriptomic analysis of hybrids and their progenitors

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

Rendered fromHybridExpress.Rmdusingknitr::rmarkdownon Nov 20 2024.

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