├── .gitignore ├── Dockerfile ├── Example_Data ├── NA19240_chr21_39000000-40000000.bam ├── NA19240_chr21_39000000-40000000.bam.bai ├── NA19240_chr21_39000000-40000000_MethylationCalls.tsv ├── NA19240_chr21_phased.vcf ├── chr21.fa └── chr21.fa.fai ├── LICENSE ├── README.md ├── docs └── images │ ├── NanoMethPhase.png │ ├── NanoMethPhaseFlowChart.png │ └── phased_IGV.png ├── envs └── environment.yaml ├── nanomethphase.py ├── nanomethphase ├── DSS_DMA.R ├── __init__.py └── __main__.py ├── scripts ├── Bin_CpG_Ratio.py ├── Binomial_test.py ├── Calculate_Average_BaseQuality.py ├── ComparePartialMethylationAtDMRsToAdjacentUsingLimma.R ├── CountReadsAtSNV.py ├── Find_Reads_with_Specific_SNV.py ├── Finding_Overlaps_Nearest.py ├── NanopolishMethylationCallsToSam_ViceVersa.py ├── PartialCpGMethylationAtDMRandAdjacent.py ├── PartialMethylation_AtDMR.sh ├── Read_Stat_After_PhasingNanoMethPhase.py ├── Trio_To_PhaseVCF_4FemaleChild.sh └── Trio_To_PhaseVCF_4MaleChild.sh ├── setup.cfg └── setup.py 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