├── .editorconfig ├── .gitattributes ├── .github ├── linters │ ├── .flake8 │ ├── .lintr │ └── .yamllint.yml └── workflows │ ├── conventional-prs.yml │ ├── main.yml │ └── release-please.yml ├── .gitignore ├── LICENSE ├── README.md ├── config ├── config.yml ├── config_github.yml ├── config_mprann.yml ├── samples.tsv ├── samples_github.tsv ├── sbatch.yml ├── tests.tsv └── tests_github.tsv ├── docs ├── Makefile ├── authors.rst ├── conf.py ├── contributing.rst ├── environment.yml ├── faq.rst ├── history.rst ├── index.rst ├── install.rst ├── license.rst ├── make.bat ├── overview.rst ├── quickstart.rst └── todo_list.rst ├── resources ├── A.bed.gz ├── B.bed.gz ├── README.md ├── demo │ ├── README.md │ ├── example_labels.tsv │ └── example_sequences.fa ├── example.fa ├── example.fa.fai ├── example.fa.genome ├── satmut_examples │ ├── GRCh38_ALL.tsv │ ├── GRCh38_BCL11A.tsv.gz │ ├── GRCh38_F9.tsv.gz │ ├── GRCh38_FOXE1.tsv.gz │ ├── GRCh38_GP1BA.tsv.gz │ ├── GRCh38_HBB.tsv.gz │ ├── GRCh38_HNF4A.tsv.gz │ ├── GRCh38_IRF4.tsv.gz │ ├── GRCh38_IRF6.tsv.gz │ ├── GRCh38_LDLR.tsv.gz │ ├── GRCh38_LDLR_2.tsv.gz │ ├── GRCh38_LRLR.tsv.gz │ ├── GRCh38_LRLR_2.tsv.gz │ ├── GRCh38_MSMB.tsv.gz │ ├── GRCh38_MYC_rs11986220.tsv.gz │ ├── GRCh38_MYC_rs6983267.tsv.gz │ ├── GRCh38_PKLR_24.tsv.gz │ ├── GRCh38_PKLR_48.tsv.gz │ ├── GRCh38_RET.tsv.gz │ ├── GRCh38_SORT1.tsv │ ├── GRCh38_SORT1.tsv.gz │ ├── GRCh38_SORT1_2.tsv.gz │ ├── GRCh38_TCF7L2.tsv.gz │ ├── GRCh38_TERT_GBM.tsv.gz │ ├── GRCh38_TERT_HEK.tsv.gz │ ├── GRCh38_UC88.tsv.gz │ ├── GRCh38_ZFAND3.tsv.gz │ ├── GRCh38_ZRSh-13.tsv.gz │ └── GRCh38_ZRSh-13h2.tsv.gz ├── test1.fa.gz └── test1.fa.gz.fai └── workflow ├── Snakefile ├── envs ├── deepexplain_gpu.yml ├── deeplift_gpu.yml ├── default.yml ├── legnet.yml ├── negative_training_sampler.yml ├── plot_ism_regions.yaml ├── plot_satmut.yaml ├── plot_satmut_regions.yaml ├── samtools.yaml ├── tensorflow.yml ├── tfmodisco-lite.yml └── tfmodisco.yml ├── report ├── images │ └── bih_logo.png └── workflow.rst ├── 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