MANIFEST.in
README.md
setup.py
SigProfilerTopography/Topography.py
SigProfilerTopography/__init__.py
SigProfilerTopography.egg-info/PKG-INFO
SigProfilerTopography.egg-info/SOURCES.txt
SigProfilerTopography.egg-info/dependency_links.txt
SigProfilerTopography.egg-info/not-zip-safe
SigProfilerTopography.egg-info/requires.txt
SigProfilerTopography.egg-info/top_level.txt
SigProfilerTopography/lib/nucleosome/AvailableNucleosomeOccupancyFiles.txt
SigProfilerTopography/lib/replication/GSM923442_hg19_wgEncodeUwRepliSeqMcf7PkRep1.bed
SigProfilerTopography/lib/replication/GSM923442_hg19_wgEncodeUwRepliSeqMcf7ValleysRep1.bed
SigProfilerTopography/lib/replication/GSM923442_hg19_wgEncodeUwRepliSeqMcf7WaveSignalRep1.wig
SigProfilerTopography/lib/transcripts/GRCh37_transcripts.txt
SigProfilerTopography/lib/ucscgenome/hg19ChromSizesDict.txt
SigProfilerTopography/lib/ucscgenome/hg38ChromSizesDict.txt
SigProfilerTopography/source/commons/AverageNucleosomeOccupancySignalArrays.py
SigProfilerTopography/source/commons/DataPreparationCommons.py
SigProfilerTopography/source/commons/NucleosomeOccupancySignalCountArrays.py
SigProfilerTopography/source/commons/NucleosomeOccupancySignalCountArraysAndFigures.py
SigProfilerTopography/source/commons/PartitionIndelsData.py
SigProfilerTopography/source/commons/PartitionNucleosomeOccupancyData.py
SigProfilerTopography/source/commons/PartitionSinglePointMutationsData.py
SigProfilerTopography/source/commons/TopographyCommons.py
SigProfilerTopography/source/commons/__init__.py
SigProfilerTopography/source/nucleosomeoccupancy/NucleosomeOccupancyAnalysis.py
SigProfilerTopography/source/nucleosomeoccupancy/NucleosomeOccupancyAnalysis_Indels.py
SigProfilerTopography/source/nucleosomeoccupancy/NucleosomeOccupancyAnalysis_SPMs_SignatureBased.py
SigProfilerTopography/source/nucleosomeoccupancy/NucleosomeOccupancyAnalysis_SPMs_SignatureBased_Indels.py
SigProfilerTopography/source/nucleosomeoccupancy/NucleosomeOccupancyAnalysis_Subs_Indels.py
SigProfilerTopography/source/nucleosomeoccupancy/__init__.py
SigProfilerTopography/source/plotting/NucleosomeOccupancyAverageSignalFigures.py
SigProfilerTopography/source/plotting/ProcessivityFigures.py
SigProfilerTopography/source/plotting/ReplicationTimeNormalizedMutationDensityFigures.py
SigProfilerTopography/source/plotting/TranscriptionReplicationStrandBiasFigures.py
SigProfilerTopography/source/plotting/__init__.py
SigProfilerTopography/source/processivity/ProcessivityAnalysis.py
SigProfilerTopography/source/processivity/__init__.py
SigProfilerTopography/source/replicationstrandbias/ReplicationStrandBiasAnalysis.py
SigProfilerTopography/source/replicationstrandbias/__init__.py
SigProfilerTopography/source/replicationtime/ReplicationTimeAnalysis.py
SigProfilerTopography/source/replicationtime/__init__.py
SigProfilerTopography/source/transcriptionstrandbias/TranscriptionStrandBiasAnalysis.py
SigProfilerTopography/source/transcriptionstrandbias/__init__.py