Scripts were used to produce the results found in the paper Stoiber et. Al "Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila"

DE_IDR_commands.R
        Reads gene_counts files (as created by htseq-counts) from samples and controls directories and runs DESeq on each sample followed by running IDR on all samples together.
paper_numbers.R
        Produces general numbers reported in the text.
paper_numbers.hnRNPs.R
        Produces numbers pertaining to UCGs, 3' UTR genes and unique binding.
num_trans_bound.R
        Produces table with significance of HOT RNAs.
PPI_overlap.R
        Produce numbers pertaining to the interaction of protein-protein and protein-RNA interactions.
create_mer_dist.py
        Create distribution of k-mers from an annotation.
analyze_motif_dists.py
        Create motifs based on the enrichment compared to expressed genes in the motif distribution.
predict_binding.py
        Predict the binding based solely on motif presense for each RBP.