SpliceHarmonization: a harmonized method for identifying RNA splicing events in therapeutics for splicing modulation

GitHub link: https://github.com/interactivereport/SpliceHarmonization Data Release: simulation_data: Demonstrates the processed splicing event simulation. simulation_data├── bam (# all simulated bam files for splicing analysis)├── fasta│ ├── combined_alt.fasta│ ├── combined_ref.fasta│ └── true_event_df.csv (# true simulated splicing event)├── simulation_num_{counts}_{alternative2control ratio} SMN2_public_dataset: Contains all splicing analyses for one SMN2 public dataset (SRP334251), including rMATS, LeafCutter, MAJIQ, and SpliceHarmonization. SMN2_public_dataset├── Original_res│ ├── bam # (bam files removed due to size limitation, happy to disuccss!)│ ├── leafcutter│ ├── majiq│ ├── rmats│ └── stringtie└── SpliceHarmonization_res └── {Comparison} ├── harm ├── harm_run_1.e.log ├── harm_run_1.o.log ├── harm_run_2.e.log ├── harm_run_2.o.log ├── harm_run_3.e.log ├── harm_run_3.o.log ├── harm_run_4.e.log ├── harm_run_4.o.log ├── junction_prep ├── out │ ├── all_cleaned.csv │ ├── all_gene │ │ ├── {gene_names}.csv (# events output for each gene) │ └── mxe ├── run1.sh ├── run2.sh ├── run3.sh └── run4.sh simulation_validation: Contains all splicing analyses for a simulation dataset, including rMATS, LeafCutter, MAJIQ, and SpliceHarmonization. simulation_validation├── Original_res│ ├── leafcutter│ ├── majiq│ ├── rmats│ └── stringtie└── SpliceHarmonization_res ├── {Comparison} │ ├── harm │ ├── harm_run_1.e.log │ ├── harm_run_1.o.log │ ├── harm_run_2.e.log │ ├── harm_run_2.o.log │ ├── harm_run_3.e.log │ ├── harm_run_3.o.log │ ├── harm_run_4.e.log │ ├── harm_run_4.o.log │ ├── junction_prep │ ├── out │ │ ├── all_cleaned.csv │ │ ├── all_gene │ │ │ ├── {gene_names}.csv (# events output for each gene) │ │ ├── introns.csv │ │ └── mxe └── FinalMetric.csv (# summary evaluation information) Files/folders in bold are final outputs