├── .github └── workflows │ ├── merge_test.yaml │ └── publish.yaml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── make.bat └── source │ ├── _images │ ├── RNA004_mapq0_HEK293T.jpg │ ├── RNA004_mapq0_Hct116.jpg │ ├── RNA004_mapq20_HEK293T.jpg │ ├── RNA004_mapq20_Hct116.jpg │ ├── arabidopsis_hek293t_mixtures.png │ └── m6anet_virc_roc_pr.png │ ├── citing.rst │ ├── cmd.rst │ ├── conf.py │ ├── help.rst │ ├── index.rst │ ├── installation.rst │ ├── quickstart.rst │ ├── release_notes.rst │ ├── rna004_release_note.rst │ └── training.rst ├── figures └── m6anet_logo.png ├── m6anet ├── __init__.py ├── deprecated │ ├── __init__.py │ ├── compute_norm_factors.py │ ├── dataprep.py │ ├── inference.py │ └── train.py ├── model │ ├── __init__.py │ ├── configs │ │ ├── model_configs │ │ │ ├── m6anet.toml │ │ │ └── prod_pooling_signal.toml │ │ └── training_configs │ │ │ └── m6anet_train_config.toml │ ├── model.py │ ├── model_blocks │ │ ├── __init__.py │ │ ├── blocks.py │ │ └── pooling_blocks.py │ ├── model_states │ │ ├── rna002_arabidopsis_virc.pt │ │ ├── rna002_hct116.pt │ │ ├── rna004_hek293t_glori.pt │ │ └── rna004_hek293t_m6ace.pt │ └── norm_factors │ │ ├── rna002_arabidopsis_virc.joblib │ │ └── rna002_hct116.joblib ├── scripts │ ├── __init__.py │ ├── compute_norm_factors.py │ ├── convert.py │ ├── dataprep.py │ ├── inference.py │ └── train.py ├── tests │ ├── conftest.py │ ├── data │ │ ├── data.indiv_proba.csv.gz │ │ ├── data.info │ │ ├── data.info.labelled │ │ ├── data.json │ │ ├── data.site_proba.csv.gz │ │ ├── eventalign.index │ │ ├── eventalign.txt │ │ └── sample_config.toml │ ├── test_dataprep.py │ └── test_inference.py └── utils │ ├── __init__.py │ ├── builder.py │ ├── constants.py │ ├── data_utils.py │ ├── dataprep_utils.py │ ├── helper.py │ ├── inference_utils.py │ ├── loss_functions │ ├── __init__.py │ └── loss_functions.py │ ├── norm_utils.py │ ├── sampler_utils.py │ └── training_utils.py └── setup.py 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