Eco80 NNPs

The objective of this archive is to help users understand or reproduce the analysis in our Eco80 NNP paper. This archive is not software and is written to minimum standards of data analysis transparency and reproducability. Users should be very careful implementing scripts or programs outside of the specific environments described in section 3.  You will find 4 things in this archive:

(1) Raw data, processed data, figures.
(2) Code to analyze the data and make figures
(3) As much as possible, information to to specify the original environment used to analyze the data and instructions for reconstituting the environment. It is fairly complex, and I am not an expert in reproducable data analysis and I am trying to learn. However, I hope enough enough information is provided via snakemake wrappers, scripts, yamls, and this readme that an expert in the area can reconstitute my analysis. Questions can be directed to jus841@psu.edu.
(4) Data tables that are compatible with the RNAstructure package, which contain adjustments to the 1 M NaCl nearest neighbor model as described in our paper. These data tables can be copied and used at the users discretion. However, users should limit their analysis to intermolecular structure prediction at 37 C.

Note that this archive contains a modified version of Dr. David Tack's StructureFold2, copied and modified according to the MIT licence (https://github.com/StructureFold2/StructureFold2).