Perform analysis of mRNA folding bias (Local Folding Energy) based on randomization experiments. See publication (Peeri and Tuller 2020) for description of methods.
Important source files:
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taxonomy.py -- Create multiple-species plots, based on taxonomic tree or PCA
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profile_plots.py -- Create plot for individual species
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tree_traits_effects_analysis_with_taxgroups.r -- Perform GLS regression and other analyses for multiple species based on phylogenetic tree
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config.py -- Configuration parameters (including database connections, etc.)
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r-rnafold -- Singularity recipe for initializing container with R environment