anampc/Ofav_NH4_SH: Release for zenodo

This repository contains data and analysis scripts for the manuscript: ## Increased Algal Symbiont Density Reduces Host Immunity in a Threatened Caribbean Coral Species, *Orbicella faveolata*<br> #### Authors: Lauren E. Fuess, Ana M. Palacio-Castro, Caleb C. Butler, Andrew C. Baker, Laura D. Mydlarz<br> #### Journal: _Front. Ecol. Evol_ [doi:10.3389/fevo.2020.572942](https://doi.org/10.3389/fevo.2020.572942) ----- ### Description: This repository: * Calculates the symbiont to host cell ratio (S/H) in *O. faveolata* corals, and<br> * Tests if corals exposed to elevated NH4 (N) present higher S/H than corals maintained under ambient concentrations (C) ### Contents:<br> #### Scripts:<br> * **SH_script.Rmd:** R script that imports the real-time PCR (qPCR) data and<br> calculates the S/H cell ratio using the StepOne program (https://github.com/jrcunning/steponeR). #### Data:<br> * **Data:** Folder containing the amplification CTs for each coral sample obtained from the qPCR machine. * **Outputs:** Folder contained exported graphs (Figure 1), S/H cell ratio values and outputs of post-hoc Tukey comparisons. * **Sample_Plates.csv:** File containing the sample treatment information (Coral colony, treatment) and the qPCR plate were each sample was run.<br> &lt;/br&gt;