Updated README with paper title and abstract

README.md

@@ -1,6 +1,42 @@
-# Project title
 
+# Overview
 
-## Abstract
+This repo contains code and data used in the paper "HybridExpress: 
+an R/Bioconductor package for comparative transcriptomic analyses of 
+hybrids and their progenitors"
 
 
+Reproducible reports for all the analyses we performed are available as 
+a Quarto book at <https://almeidasilvaf.github.io/HybridExpress_paper/>.
+
+
+## Summary
+
+- Hybridization, the process of crossing individuals from diverse 
+genetic backgrounds, plays a pivotal role in evolution, biological 
+invasiveness, and crop breeding. 
+
+- At the transcriptional level, hybridization often leads to complex 
+non-additive effects, presenting challenges for understanding its 
+consequences. Although standard transcriptomic analyses exist to compare 
+hybrids to their progenitors, such analyses have not been implemented in a 
+software package, hindering reproducibility.
+
+- We introduce *HybridExpress*, an R/Bioconductor package designed to 
+facilitate the analysis, visualization, and comparison of gene expression 
+patterns in hybrid triplets (hybrids and their progenitors). *HybridExpress* 
+provides users with a user-friendly and comprehensive workflow that includes 
+all standard comparative analyses steps, including data normalization, 
+calculation of midparent expression values, sample clustering, 
+expression-based gene classification into categories and classes, 
+and overrepresentation analysis for functional terms. 
+
+- We illustrate the utility of *HybridExpress* through comparative 
+transcriptomic analyses of cotton allopolyploidization and rice root trait 
+heterosis. *HybridExpress* is designed to streamline comparative transcriptomic 
+studies of hybrid triplets, advancing our understanding of evolutionary 
+dynamics in allopolyploids, and enhancing plant breeding strategies.
+
+
+**Keywords:** gene expression, transcriptomic shock, allopolyploidy, hybrid vigor, expression-level dominance.
+