From 5c114fe69f48b95d8bfeb5ae629717bb66853347 Mon Sep 17 00:00:00 2001 From: almeidasilvaf Date: Fri, 23 Feb 2024 11:46:08 +0100 Subject: [PATCH] Revised text in vignette --- vignettes/HybridExpress.Rmd | 27 ++++++++++++++++----------- 1 file changed, 16 insertions(+), 11 deletions(-) diff --git a/vignettes/HybridExpress.Rmd b/vignettes/HybridExpress.Rmd index 4e7c315..64956e2 100644 --- a/vignettes/HybridExpress.Rmd +++ b/vignettes/HybridExpress.Rmd @@ -29,25 +29,30 @@ knitr::opts_chunk$set( # Introduction -The formation of hybrids through the fusion of distinct genomes and subsequent -genome duplication in cases of allopolyploidy represents a significant -evolutionary event with complex effects on cellular biology, particularly gene expression. The impact of such genome mergings and duplications on -transcription remain incompletely understood. To bridge this gap, we introduce __HybridExpress__, a comprehensive package designed to facilitate the -comparative transcriptomic analysis of hybrids and their progenitor species. -__HybridExpress__ is tailored for RNA-Seq data derived from an -'experimental trio': the hybrid organism and its two parental species. +The formation of hybrids through the fusion of distinct genomes and +subsequent genome duplication (in cases of allopolyploidy) represents a +significant evolutionary event with complex effects on cellular biology, +particularly gene expression. The impact of such genome mergings and +duplications on transcription remain incompletely understood. To bridge this +gap, we introduce __HybridExpress__, a comprehensive package designed to +facilitate the comparative transcriptomic analysis of hybrids and their +progenitor species. __HybridExpress__ is tailored for RNA-Seq data derived +from a 'hybrid triplet': the hybrid organism and its two parental species. This package offers a suite of intuitive functions enabling researchers to perform differential expression analysis with ease, generate principal -component analysis (PCA) plots for visualizing gene expression trends, +component analysis (PCA) plots to visualize sample grouping, categorize genes into 12 distinct expression pattern groups -(as in @rapp2009genomic), and conduct in-depth functional analyses. +(as in @rapp2009genomic), and conduct functional analyses. Acknowledging the potential variability in cell and transcriptome size across species and ploidy levels, __HybridExpress__ incorporates features for rigorous normalization of count data. Specifically, it allows for the -integration of spike-in standards directly into the normalization process, +integration of spike-in controls directly into the normalization process, ensuring accurate transcriptome size adjustments when these standards are present in the RNA-Seq count data (see full methodology in @coate2023beyond). -By offering these capabilities, __HybridExpress__ provides a robust toolset for unraveling the intricate effects of genome doubling and merging on hybrid gene expression, paving the way for novel insights into the cellular biology of hybrid organisms. +By offering these capabilities, __HybridExpress__ provides a robust +tool set for unraveling the intricate effects of genome doubling and +merging on gene expression, paving the way for novel insights into the +cellular biology of hybrid organisms. # Installation