hawaiian_drosophilidae_expression_2021

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

Contents

Manuscript files

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.

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/

Results

Figures are printed to the directory figures_and_panels/

Environment

Information on the R environment used to perform the comprative analyses is in the file

r_session_info.txt