├── .gitignore ├── LICENSE ├── README.md ├── Snakefile ├── conda_requirements.txt ├── conda_wrapper ├── docs └── basic_alt_splicing_patterns.jpg ├── example ├── .gitignore ├── data.tar.gz ├── group_1.txt ├── group_2.txt ├── gs689_1_corrected.sam ├── gs689_2_corrected.sam ├── gs689_3_corrected.sam ├── pc3e_1_corrected.sam ├── pc3e_2_corrected.sam ├── pc3e_3_corrected.sam ├── samples_N2_R0_abundance.esp └── samples_N2_R0_updated.gtf ├── example_out ├── .gitignore └── rmats_long │ └── results_by_gene │ └── ENSG00000204580.14 │ ├── 2_0_abundance.png │ └── 2_0_structure.png ├── example_out_asm ├── .gitignore └── rmats_long │ └── results_by_gene │ └── ENSG00000198561.16 │ ├── 0_11_abundance.png │ ├── 0_11_graph.png │ ├── 0_11_in_gene.png │ └── 0_11_structure.png ├── example_out_from_abun ├── .gitignore └── results_by_gene │ └── ENSG00000204580.14 │ ├── ENSG00000204580.14_abundance.png │ └── ENSG00000204580.14_structure.png ├── install ├── run_snakemake ├── run_tests ├── scripts ├── FindAltTSEvents.py ├── add_novel_transcripts_to_gtf.py ├── calculate_isoform_proportion.py ├── classify_isoform_differences.py ├── clean_espresso_gtf.py ├── count_reads_for_asms.py ├── count_significant_isoforms.py ├── create_gtf_from_asm_definitions.py ├── detect_differential_isoforms.R ├── detect_differential_isoforms.py ├── detect_splicing_events.py ├── organize_alignment_info_by_gene_and_chr.py ├── organize_gene_info_by_chr.py ├── plot_gene_sets.R ├── plot_splice_graph.py ├── rmats_long.py ├── rmats_long_utils.py ├── run_drimseq.R ├── run_stat_model.py ├── simplify_alignment_info.py ├── visualize_isoforms.R ├── visualize_isoforms.py └── visualize_summary.R ├── set_env_vars.sh ├── shiny ├── README.md ├── clear_1px.png ├── conda_requirements.txt ├── find_gene_id_name.py ├── get_isoform_sequence.py ├── run.R ├── server.R └── ui.R ├── snakemake_config.yaml ├── snakemake_profile ├── .gitignore ├── cluster_cancel.py ├── cluster_commands.py ├── cluster_status.py ├── cluster_submit.py ├── config.v8+.yaml └── try_command.py └── tests ├── __init__.py ├── asm_detection ├── .gitignore ├── __init__.py └── test.py ├── asm_read_counts ├── .gitignore ├── __init__.py └── test.py ├── base_test.py ├── filtered_asms ├── .gitignore ├── __init__.py └── test.py ├── gene_isoforms ├── .gitignore ├── __init__.py └── test.py ├── isoform_diffs ├── .gitignore ├── __init__.py └── test.py ├── no_counts_replicate ├── .gitignore ├── __init__.py └── test.py ├── runner.py ├── se_asm ├── .gitignore ├── __init__.py └── test.py ├── se_gene ├── .gitignore ├── __init__.py └── test.py └── significance_filters ├── .gitignore ├── __init__.py └── test.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Xinglab/rMATS-long/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 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