This repostiory contains the data and code for a future manuscript on tissue-specific expression evolution in Hawaiian Drosophila and Scaptomyza flies.
There is an accompanying data visualization that can be found here: https://shchurch.shinyapps.io/hawaiian_fly_dataviz_2021
and here: https://github.com/shchurch/hawaiian_fly_dataviz_2021
The main text and supplementary methods can be reproduced from the Rmarkdown files
Hawaiian_transcriptome_manuscript.Rmd
Hawaiian_transcriptome_supplement.Rmd
In addition, the supplementary methods Rmd file contains all the script calls required to reproduce all analyses.
All analyses script files are including in the directory analysis.
This includes input data files downloaded from https://flybase.org/ and other online repositories, under analysis/data.
It also includes scripts for each stage of the analysis in the following directories:
The code used to map and annotate RNA reads is located in the directories
analysis/agalma/
analysis/BLAST/
There are also several files containing collection and sequencing data in the directory expression_methods_data/
Code to import the results of these analysis into R is located in the files
analysis/read_in_expression.R
Code to perform all comparative analyses are located in the directories
analysis/differential_expression/
analysis/ANOVA/
analysis/phylogenetic_expression/
analysis/head_analyses/
Figures are printed to the directory figures_and_panels/
Information on the R environment used to perform the comprative analyses is in the file
r_session_info.txt