├── .gitignore ├── LICENSE ├── README.md ├── bin └── isoseqsim ├── example ├── gene_annotation.gtf ├── genome.fasta ├── genotype.vcf └── input │ ├── gene_annotation.gtf │ ├── genome.fasta │ └── genotype.vcf └── utilities ├── 3_end_completeness.PacBio-P4-C2.tab ├── 3_end_completeness.PacBio-P5-C3.tab ├── 3_end_completeness.PacBio-P6-C4.tab ├── 3_end_completeness.PacBio-Sequel.tab ├── 3_end_completeness.Perfect.tab ├── 5_end_completeness.PacBio-P4-C2.tab ├── 5_end_completeness.PacBio-P5-C3.tab ├── 5_end_completeness.PacBio-P6-C4.tab ├── 5_end_completeness.PacBio-Sequel.tab ├── 5_end_completeness.Perfect.tab ├── py_extract_completeness.py ├── py_isoseqsim_generate_apa_event.py ├── py_isoseqsim_generate_ats_event.py ├── py_isoseqsim_generate_expr_matrix.py ├── py_isoseqsim_generate_expr_matrix_ase.py ├── py_isoseqsim_generate_expr_matrix_by_fixed_count.py ├── py_isoseqsim_generate_fusion_event.py ├── py_isoseqsim_generate_haplotype_fa.py ├── py_isoseqsim_gpd2fa_apa.py ├── 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