Index of /kundaje/marinovg/oak/various/code/bisulfite

	Name	Last modified	Size	Description
	Parent Directory		-
	AverageMethylationPerRegion-V2.py	2025-05-22 03:16	4.0K
	AverageMethylationPerRegion.py	2019-04-19 11:18	3.2K
	AverageNMIfromBED.py	2025-05-28 09:20	5.0K
	AverageSingleMoleculeEntropy.py	2018-10-04 17:25	3.2K
	BisMarckMerge.py	2025-04-19 03:52	2.1K
	BismarckCXreportToWig-complement.py	2017-07-26 08:24	1.5K
	BismarckCXreportToWig.py	2017-07-24 23:44	1.9K
	BismarckCovBias.py	2025-05-24 15:03	4.3K
	BismarckSequenceContextFilter.py	2025-04-15 23:53	3.4K
	BismarckSequenceContextPlusMinusSplit.py	2025-05-14 07:10	2.4K
	BismarckStats.py	2017-07-11 16:59	1.8K
	CtoT_HISAT-3N-extract.py	2025-03-04 17:28	15K
	MetagenePlot2D.py	2018-12-05 19:17	8.9K
	MetanucleosomePlot1D.py	2019-08-16 09:57	5.6K
	MetanucleosomePlot2D.py	2018-11-28 00:00	6.3K
	MethylationPercentageContext.py	2018-04-24 09:00	5.3K
	MethylationPercentageSmooth-dSMF.py	2025-05-22 03:03	5.1K
	MethylationPercentageSmooth-nano.py	2018-04-28 09:15	2.4K
	MethylationPercentageSmooth.py	2018-04-28 08:11	2.1K
	NanoporeTSVMappingStats.py	2019-04-06 00:45	1.8K
	ONT_methylation_sequence_bias.py	2018-08-10 09:14	5.3K
	ONT_methylation_status_of_neighboring_positions.py	2018-08-10 10:55	4.9K
	ONT_read_length_methylation.py	2018-08-08 09:22	1.5K
	ReadsTSVPerBaseMethylationStats.py	2023-05-13 14:54	2.0K
	SMAC-footprints-from-methylation-reads-tsv-SecondFormat.py	2018-05-03 13:40	12K
	SMAC-footprints-from-methylation-reads-tsv-all-sites.py	2018-12-05 19:53	8.8K
	SMAC-footprints-from-methylation-reads-tsv-tabix-all-sites.py	2025-04-18 17:34	11K
	SMAC-footprints-from-methylation-reads-tsv-tabix-kmeans-all-sites.py	2025-05-31 10:37	13K
	SMAC-footprints-from-methylation-reads-tsv-tabix-kmeans.py	2025-04-18 14:36	19K
	SMAC-footprints-from-methylation-reads-tsv-tabix.py	2019-11-08 12:34	19K
	SMAC-footprints-from-methylation-reads-tsv.py	2018-05-04 13:41	18K
	SMAC-seq-resolution-motifs.py	2018-09-18 13:23	2.8K
	SMAC-seq-resolution.py	2018-08-10 15:45	1.7K
	SMRTN6mAToBismarckCov.py	2018-04-17 06:19	2.1K
	SingleMoleculeCorrelation-JSD-matrix.py	2018-08-08 15:19	9.2K
	SingleMoleculeCorrelation-NMI-matrix-C-BAM-to-heatmap.py	2025-05-25 13:04	2.0K
	SingleMoleculeCorrelation-NMI-matrix-C-BAM.py	2025-05-25 13:03	7.8K
	SingleMoleculeCorrelation-NMI-matrix.py	2018-12-03 21:00	9.8K
	SingleMoleculeCorrelation-TFsTombo1.3.py	2018-07-06 16:45	11K
	SingleMoleculeCorrelation-annotateTSSs-V2.py	2018-11-30 15:09	3.2K
	SingleMoleculeCorrelation-annotateTSSs-expression-correlation.py	2018-10-08 15:46	4.3K
	SingleMoleculeCorrelation-annotateTSSs-scatter_plot.py	2018-11-30 10:13	3.5K
	SingleMoleculeCorrelation-annotateTSSs-with-HiC.py	2018-10-08 13:01	4.0K
	SingleMoleculeCorrelation-annotateTSSs-with-expression.py	2018-12-17 12:59	4.3K
	SingleMoleculeCorrelation-annotateTSSs.py	2018-07-06 16:12	3.1K
	SingleMoleculeCorrelation-empirical-quantiles.py	2018-11-30 14:29	15K
	SingleMoleculeCorrelation-empirical.py	2018-07-23 07:08	13K
	SingleMoleculeCorrelation.py	2018-07-06 16:17	9.0K
	SingleMoleculeCorrelation_NMI_matrix.c	2019-01-24 23:11	496K
	SingleMoleculeCorrelation_NMI_matrix.pyx	2019-01-24 23:05	9.9K
	SingleMoleculeCorrelation_NMI_matrix.so	2019-01-24 23:11	1.0M
	SingleMoleculeCorrelation_NMI_matrix_cython.py	2019-01-24 23:10	2.6K
	SingleMoleculeCorrelation_NMI_matrix_cython_setup.py	2019-01-24 23:11	233
	SingleMoleculeStatesOverPositions-order-states.py	2018-11-25 23:54	2.4K
	SingleMoleculeStatesOverPositions.py	2018-11-26 02:50	3.4K
	SingleMoleculeStatesOverPositionsInARegion----broken.py	2018-12-10 18:41	15K
	SingleMoleculeStatesOverPositionsInARegion-kmeans.py	2018-12-10 21:17	18K
	TomboSingleReadsExtract-V2.py	2018-05-25 08:08	7.2K
	TomboSingleReadsExtract-tombo_de_novo-1.5-py3.py	2023-02-02 14:40	17K
	TomboSingleReadsExtract-tombo_de_novo-1.5.py	2019-10-20 23:45	17K
	TomboSingleReadsExtract-tombo_de_novo.py	2023-11-06 01:39	16K
	TomboSingleReadsExtract.py	2018-05-14 18:02	7.1K
	TomboStatsParse.py	2018-04-30 17:13	4.0K
	annotatePlusOneNucleosomes.py	2018-11-26 13:47	3.9K
	build/	2019-01-24 23:11	-
	coverage_to_wig.py	2019-05-05 04:25	4.4K
	coveragesimulation.py	2024-11-08 15:46	1.6K
	dSMF-footprints.py	2025-04-18 14:48	14K
	doradoBAMextract-plus-only.py	2023-11-18 10:53	17K
	doradoBAMextract.py	2024-09-21 23:21	18K
	filterFullyMethylatedReads.py	2018-11-18 08:22	6.3K
	kmeans_tsv.R	2018-12-01 14:07	839
	megalodon-to-single_line.py	2023-05-14 10:57	5.8K
	methylation-reads-tsv-nanopolish-CpG-to_coverage.py	2018-06-03 04:23	2.6K
	methylation-reads-tsv-to_coverage.py	2023-11-19 16:33	9.8K
	methylation-reads-tsv-to_single_line.py	2020-03-16 17:15	2.8K
	methylation-tsv-combine-mods.py	2019-01-04 07:55	2.8K
	methylation_single_base_to_bedGraph.py	2018-04-28 09:52	1.9K
	minimapBAMextractCT.py	2025-04-01 15:36	7.5K
	signalAroundPeaks-nano-V2.py	2026-02-17 20:44	8.1K
	signalAroundPeaks-nano-tabix.py	2025-04-17 21:04	7.0K
	signalAroundPeaks-nano.py	2025-05-31 06:19	8.2K