Data, code, and results for our paper Identification of core, conditional and crosstalk components of tomato heat stress response using integrative transcriptomics and orthology (https://doi.org/10.21203/rs.3.rs-4337825/v1). If you use any of our code or results in a scientific publication, we would be grateful if you cite the paper.

This repository uses git LFS for all files matching *.lfs.*.

It is structured in the following folders:

• analyses: contains code, input, and output of individual analyses. Some analyses depend on output of previous steps, hence they are numbered. Within each analysis, scripts are also numbered to explain in which order they were/need to be executed.
• data: original input data for the manuscript. The README describes how they were obtained.
• figures: SVG and PDF versions of the figures used in the final manuscript (composed and edited with Inkscape.
• plots: all plots generated by the different analyses, named by the analysis they belong to (e.g. the plot 4.3_oldest_orthologs.pdf is a result of analysis 4). output/plots in each analysis links to this folder.
• shiny_app: code for the interactive companion web app at https://szymanskilab.shinyapps.io/tomato-rna-meta
• supplement: supplementary data to the manuscript.

More information can be found in the READMEs of the respective subfolders.