This repo contains code I've used for various splicedice analysis. See also my splicedice notes file (protected; access provided on request).
| Project | Milestone | Link |
|---|---|---|
| Identify validation data for intron retention | Discrepancies between my results and Javier's | |
| Identify validation data for intron retention | Figure out which version of mesa Javier used | Comparison |
| Identify validation data for intron retention | Identical results using older code | 2025 11 07 intron retention replication retry.md |
| Identify validation data for intron retention | Identical results using slighly less old code | 2025 11 13 intron retention replication retry with f833a58.md |
| Identify validation data for intron retention | Identical results using the latest code and Javier's scripts | 2025 11 18 intron retention replication retry with da045c4.md |
| Identify validation data for intron retention | Identical results using the latest code with my commands and Javier's scripts | 2025 12 01 intron retention.md |
| Identify validation data for intron retention | Results differ based on genome build (Homo_sapiens.GRCh38.dna.primary_assembly.fa instead of GRCh38.primary_assembly.genome.fa) | 2025 12 02 intron retention.md |
| Identify validation data for intron retention | Summary: discrepancy has been resolved; I can proceed with defining validation sets | 2025 12 03 intron retention discrepancy conclusions.md |
| Identify validation data for intron retention | Results are documented and frozen | 2025 12 03 intron retention validation data.md |