Pending features #3
Description
Faster to implement:
F1. Merge intron retention results with junction results.
F2. Automatically create output summary and IGV files
F3. Intron Retention PSI values and rework IR of genes with majority of introns retained
F4. Output confidence intervals from hypergeometric
F5. Convert readme to .md, improve content and layout
F6. Mirror readme in the AWS S3 index.html
F7. Add final summary file (Parameters + Stats per category)
Slower to implement:
S1. R integration/PSI plotting
S2. Handle replicates
S3. Handle multiple conditions
S4. Integrate the motif analysis/U12/Size distr. pipelines