gigas-ploidy-heatwave

# gigas-ploidy-heatwave

Data and code repository for publication, "Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following marine heatwaves." The preprint on bioRXiv can be found at:

This project was funded by the National Oceanographic Partnership Program (IWG-NOPP) and investigates the impact of marine heatwaves (temperature and/or desiccation) on diploid (2n) and triploid (3n) Pacific oysters. Hatchery experiments were conducted at the Jamestown S'Klallam Point Whitney Shellfish Hatchery located on Dabob Bay, Washington, USA (47°45"N 122°50'W).

# Table of Contents
### `analyses`
Output of R markdown files listed in `code` folder

### `code`
R markdown files for each dataset analysis in `data` folder

### `data`
Raw data for each analysis. Each subfolder can be analyzed from the `gigas-ploidy-heatwave.Rproj`. Additional data processing for respirometry data was first carried out in the `data/respirometry` folder using the `respirometry.Rproj` and R markdown files listed in `data/respirometry/code`. Additional data processing for tag-seq data was first carried out in `data/tag-seq` folder using the `tag-seq.Rproj` and R markdown files listed in `data/tag-seq/code`.

### `figures`
Polished figures used in the publication

### `stats`
Output of statistical tests from R markdown files in `data` folder

### `suppl_figures`
Supplemental figures used in the publication

### `suppl_tables`
Supplemental tables detailing DEG and GOterm lists for each treatment