├── .gitattributes ├── .github ├── CODEOWNERS └── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── .gitignore ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── docs ├── CNAME ├── alternative.md ├── changelog.md ├── citing.md ├── code_of_conduct.md ├── contributing.md ├── data_api.md ├── data_preparation.md ├── demo │ ├── Eventalign_collapse_usage.ipynb │ ├── SampCompDB_usage.ipynb │ ├── SampComp_usage.ipynb │ ├── SimReads_usage.ipynb │ ├── eventalign_files │ │ ├── simulated │ │ │ ├── modified_rep_1.tsv │ │ │ ├── modified_rep_1.tsv.idx │ │ │ ├── modified_rep_1_pos.tsv │ │ │ ├── modified_rep_2.tsv │ │ │ ├── modified_rep_2.tsv.idx │ │ │ ├── modified_rep_2_pos.tsv │ │ │ ├── unmodified_rep_1.tsv │ │ │ ├── unmodified_rep_1.tsv.idx │ │ │ ├── unmodified_rep_1_pos.tsv │ │ │ ├── unmodified_rep_2.tsv │ │ │ ├── unmodified_rep_2.tsv.idx │ │ │ └── unmodified_rep_2_pos.tsv │ │ └── yeast │ │ │ ├── KO_1_eventalign_collapsed.tsv │ │ │ ├── KO_1_eventalign_collapsed.tsv.idx │ │ │ ├── KO_1eventalign_collapsed.tsv.idx │ │ │ ├── KO_2_eventalign_collapsed.tsv │ │ │ ├── KO_2_eventalign_collapsed.tsv.idx │ │ │ ├── WT_1_eventalign_collapsed.tsv │ │ │ ├── WT_1_eventalign_collapsed.tsv.idx │ │ │ ├── WT_2_eventalign_collapsed.tsv │ │ │ └── WT_2_eventalign_collapsed.tsv.idx │ ├── references │ │ ├── simulated │ │ │ ├── ref.fa │ │ │ └── ref.fa.fai │ │ └── yeast │ │ │ ├── Yeast_transcriptome.fa │ │ │ └── Yeast_transcriptome.fa.fai │ └── samples.yaml ├── index.md ├── installation.md ├── licence.md ├── output.md ├── pictures │ ├── Nanocompore_logo.png │ ├── Nanocompore_logo.svg │ ├── plot_coverage.png │ ├── plot_gmm.png │ ├── plot_position.png │ ├── plot_pvalues.png │ ├── plot_signal_split_boxenplot.png │ ├── plot_signal_violinplot.png │ ├── pvalues.png │ ├── signal_shift.png │ ├── worflow.png │ └── worflow.svg ├── plotting.md ├── plotting_api.md ├── troubleshooting.md └── usage.md ├── mkdocs.yml ├── nanocompore ├── __init__.py ├── __main__.py ├── api.py ├── common.py ├── comparisons.py ├── config.py ├── database.py ├── eventalign_collapse.py ├── gof_tests.py ├── models │ ├── __init__.py │ ├── kmers_model_RNA_r9.4_180mv.tsv │ ├── rna002_5mer_levels_v1.txt │ └── rna004_9mer_levels_v1.txt ├── plotting.py ├── postprocessing.py ├── preprocessing.py ├── remora_wrapper.py ├── run.py ├── template_config.yaml ├── transcript.py └── uncalled4.py ├── pyproject.toml ├── scripts ├── add_genomic_coords.py ├── compare_pair.py └── test_coverage.sh ├── tests ├── common.py ├── fixtures │ ├── empty.bam │ ├── empty.bam.bai │ ├── kd1.bam │ ├── kd1.bam.bai │ ├── kd1.pod5 │ ├── kd1_eventalign.db │ ├── kd1_eventalign.tsv │ ├── kd2.bam │ ├── kd2.bam.bai │ ├── kd2.pod5 │ ├── kd2_eventalign.db │ ├── kd2_eventalign.tsv │ ├── out_sampComp_sql.db │ ├── test_annotation.gtf │ ├── test_reference.fa │ ├── test_reference.fa.fai │ ├── uncalled4_reference.fa │ ├── uncalled4_reference.fa.fai │ ├── uncalled4_sample.bam │ ├── uncalled4_sample.bam.bai │ 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