├── ._travis.yml ├── .github └── workflows │ └── python-package-conda.yml ├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── MISO ├── README.txt ├── run_miso.sh └── settings │ ├── new_splice_site_events.gff │ └── plot_timmdc1_new_exon.conf ├── README.md ├── docs ├── Makefile ├── make.bat └── source │ ├── conf.py │ ├── help.rst │ ├── index.rst │ ├── installation.rst │ ├── license.rst │ ├── output.rst │ ├── pipeline.rst │ └── prepare.rst ├── drop ├── __init__.py ├── cli.py ├── config │ ├── DropConfig.py │ ├── ExportCounts.py │ ├── Genome.py │ ├── SampleAnnotation.py │ ├── SampleParams.py │ ├── __init__.py │ └── submodules │ │ ├── AberrantExpression.py │ │ ├── AberrantSplicing.py │ │ ├── MonoallelicExpression.py │ │ ├── RNAVariantCalling.py │ │ ├── Submodules.py │ │ └── __init__.py ├── demo │ ├── __init__.py │ ├── config_relative.yaml │ ├── fixPaths.py │ └── sample_annotation_relative.tsv ├── download_data.sh ├── installRPackages.R ├── modules │ ├── aberrant-expression-pipeline │ │ ├── Counting │ │ │ ├── Datasets.R │ │ │ ├── Summary.R │ │ │ ├── countReads.R │ │ │ ├── exportCounts.R │ │ │ ├── filterCounts.R │ │ │ └── mergeCounts.R │ │ ├── OUTRIDER │ │ │ ├── Datasets.R │ │ │ ├── Summary.R │ │ │ ├── pvalsOutrider.R │ │ │ ├── results.R │ │ │ └── runOutrider.R │ │ ├── Snakefile │ │ └── aberrant_expression_readme.md │ ├── aberrant-splicing-pipeline │ │ ├── Counting │ │ │ ├── 00_define_datasets_from_anno.R │ │ │ ├── 01_0_countRNA_init.R │ │ │ ├── 01_1_countRNA_splitReads_samplewise.R │ │ │ ├── 01_2_countRNA_splitReads_merge.R │ │ │ ├── 01_3_countRNA_nonSplitReads_samplewise.R │ │ │ ├── 01_4_countRNA_nonSplitReads_merge.R │ │ │ ├── 01_5_countRNA_collect.R │ │ │ ├── 02_psi_value_calculation_FraseR.R │ │ │ ├── 03_filter_expression_FraseR.R │ │ │ ├── DatasetsF.R │ │ │ ├── Summary.R │ │ │ └── exportCounts.R │ │ ├── FRASER │ │ │ ├── 04_fit_hyperparameters_FraseR.R │ │ │ ├── 05_fit_autoencoder_FraseR.R │ │ │ ├── 06_annotate_genes.R │ │ │ ├── 07_calculation_stats_FraseR.R │ │ │ ├── 08_extract_results_FraseR.R │ │ │ ├── Datasets.R │ │ │ └── Summary.R │ │ ├── Snakefile │ │ ├── aberrant_splicing_readme.md │ │ └── config.R │ ├── helpers │ │ ├── add_HPO_cols.R │ │ └── parse_subsets_for_FDR.R │ ├── mae-pipeline │ │ ├── MAE │ │ │ ├── ASEReadCounter.sh │ │ │ ├── Datasets.R │ │ │ ├── Results.R │ │ │ ├── deseq_mae.R │ │ │ ├── filterSNVs.sh │ │ │ └── gene_name_mapping.R │ │ ├── QC │ │ │ ├── DNA_RNA_matrix_plot.R │ │ │ ├── Datasets.R │ │ │ ├── create_matrix_dna_rna_cor.R │ │ │ └── deseq_qc.R │ │ ├── Snakefile │ │ └── mae_readme.md │ └── rvc-pipeline │ │ ├── GATK_BASH │ │ ├── bqsr.sh │ │ ├── changeHeader.sh │ │ ├── haplotypeCaller.sh │ │ ├── maskSingleVCF.sh │ │ └── simpleAnnotation.sh │ │ ├── Snakefile │ │ ├── countVariants │ │ ├── Datasets.R │ │ ├── Results.R │ │ └── batch_data_table.R │ │ └── rvc_readme.md ├── requirementsR.txt ├── setupDrop.py ├── template │ ├── Scripts │ │ ├── AberrantExpression │ │ │ └── Overview.R │ │ ├── AberrantSplicing │ │ │ └── Overview.R │ │ ├── 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