Index

_

__init__() (fanc.plotting.BigWigPlot method) (fanc.plotting.FeatureLayerPlot method) (fanc.plotting.GenePlot method) (fanc.plotting.GenomicDataFramePlot method) (fanc.plotting.GenomicFeaturePlot method) (fanc.plotting.GenomicFeatureScorePlot method) (fanc.plotting.GenomicFigure method) (fanc.plotting.GenomicRegionsPlot method) (fanc.plotting.GenomicVectorArrayPlot method) (fanc.plotting.HicPeakPlot method) (fanc.plotting.HicSlicePlot method) (fanc.plotting.HighlightAnnotation method) (fanc.plotting.LimitGroup method) (fanc.plotting.LinePlot method) (fanc.plotting.MirrorMatrixPlot method) (fanc.plotting.SplitMatrixPlot method) (fanc.plotting.SquareMatrixPlot method) (fanc.plotting.SymmetricNorm method) (fanc.plotting.TriangularMatrixPlot method)

A

ABCompartmentMatrix (class in fanc.architecture.compartments) ABCompartmentMatrix.ChromosomeDescription (class in fanc.architecture.compartments) ABCompartmentMatrix.MaskDescription (class in fanc.architecture.compartments) ABCompartmentMatrix.RegionDescription (class in fanc.architecture.compartments) add_chromosome() (fanc.regions.Genome method) add_contact() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) add_contacts() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) add_edge() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) add_edge_from_dict() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) add_edge_from_edge() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) add_edge_from_list() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) add_edge_simple() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) add_edges() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method)

add_filter() (fanc.pairs.FourDNucleomePairGenerator method) (fanc.pairs.HicProPairGenerator method) (fanc.pairs.PairedSamBamReadPairGenerator method) (fanc.pairs.ReadPairGenerator method) (fanc.pairs.SamBamReadPairGenerator method) (fanc.pairs.TxtReadPairGenerator method) add_mask_description() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) add_read_pairs() (fanc.pairs.ReadPairs method) add_region() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method) add_regions() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method) additional_arguments (fanc.map.Bowtie2Mapper attribute) (fanc.map.BwaMapper attribute) (fanc.map.SimpleBowtie2Mapper attribute) (fanc.map.SimpleBwaMapper attribute) AggregateMatrix (class in fanc.architecture.aggregate) algorithm (fanc.map.BwaMapper attribute) (fanc.map.SimpleBwaMapper attribute) ALIGNED (fanc.matrix.RegionMatrix attribute) all() (fanc.matrix.RegionMatrix method) anom() (fanc.matrix.RegionMatrix method) any() (fanc.matrix.RegionMatrix method) argmax() (fanc.matrix.RegionMatrix method) argmin() (fanc.matrix.RegionMatrix method) argpartition() (fanc.matrix.RegionMatrix method) argsort() (fanc.matrix.RegionMatrix method) as_bed_line() (fanc.compatibility.cooler.LazyCoolerRegion method) (fanc.pairs.LazyFragment method) (fanc.regions.LazyGenomicRegion method) as_edge() (in module fanc.matrix) as_gff_line() (fanc.compatibility.cooler.LazyCoolerRegion method) (fanc.pairs.LazyFragment method) (fanc.regions.LazyGenomicRegion method) astype() (fanc.matrix.RegionMatrix method) attributes() (fanc.compatibility.cooler.LazyCoolerRegion property) (fanc.pairs.LazyFragment property) (fanc.regions.LazyGenomicRegion property) autoscale() (fanc.plotting.SymmetricNorm method) autoscale_None() (fanc.plotting.SymmetricNorm method)

B

base (fanc.matrix.RegionMatrix attribute) baseclass() (fanc.matrix.RegionMatrix property) BEHAVED (fanc.matrix.RegionMatrix attribute) bias (fanc.matrix.Edge attribute) (fanc.matrix.LazyEdge attribute) bias_vector() (fanc.hic.Hic method) (fanc.hic.LegacyHic method) BigWigPlot (class in fanc.plotting) bin() (fanc.hic.Hic method) (fanc.hic.LegacyHic method) bin_intervals() (fanc.architecture.comparisons.ComparisonMatrix static method) (fanc.architecture.comparisons.ComparisonRegions static method) (fanc.architecture.comparisons.ComparisonScores static method) (fanc.architecture.comparisons.DifferenceMatrix static method) (fanc.architecture.comparisons.DifferenceRegions static method) (fanc.architecture.comparisons.DifferenceScores static method) (fanc.architecture.comparisons.FoldChangeMatrix static method) (fanc.architecture.comparisons.FoldChangeRegions static method) (fanc.architecture.comparisons.FoldChangeScores static method) (fanc.architecture.compartments.ABCompartmentMatrix static method) (fanc.architecture.domains.Boundaries static method) (fanc.architecture.domains.DirectionalityIndex static method) (fanc.architecture.domains.DirectionalityIndexes static method) (fanc.architecture.domains.InsulationScore static method) (fanc.architecture.domains.InsulationScores static method) (fanc.architecture.domains.RegionMultiScoreTable static method) (fanc.architecture.domains.RegionScoreParameterTable static method) (fanc.architecture.domains.RegionScoreTable static method) (fanc.compatibility.cooler.CoolerHic static method) (fanc.compatibility.juicer.JuicerHic static method) (fanc.hic.Hic static method) (fanc.hic.LegacyHic static method) (fanc.matrix.RegionMatrixContainer static method) (fanc.matrix.RegionMatrixTable static method) (fanc.matrix.RegionPairsContainer static method) (fanc.matrix.RegionPairsTable static method) (fanc.pairs.ReadPairs static method) (fanc.peaks.PeakInfo static method) (fanc.peaks.RaoPeakInfo static method) (fanc.regions.RegionsTable static method) bin_intervals_equidistant() (fanc.architecture.comparisons.ComparisonMatrix static method) (fanc.architecture.comparisons.ComparisonRegions static method) (fanc.architecture.comparisons.ComparisonScores static method) (fanc.architecture.comparisons.DifferenceMatrix static method) (fanc.architecture.comparisons.DifferenceRegions static method) (fanc.architecture.comparisons.DifferenceScores static method) (fanc.architecture.comparisons.FoldChangeMatrix static method) (fanc.architecture.comparisons.FoldChangeRegions static method) (fanc.architecture.comparisons.FoldChangeScores static method) (fanc.architecture.compartments.ABCompartmentMatrix static method) (fanc.architecture.domains.Boundaries static method) (fanc.architecture.domains.DirectionalityIndex static method) (fanc.architecture.domains.DirectionalityIndexes static method) (fanc.architecture.domains.InsulationScore static method) (fanc.architecture.domains.InsulationScores static method) (fanc.architecture.domains.RegionMultiScoreTable static method) (fanc.architecture.domains.RegionScoreParameterTable static method) (fanc.architecture.domains.RegionScoreTable static method) (fanc.compatibility.cooler.CoolerHic static method) (fanc.compatibility.juicer.JuicerHic static method) (fanc.hic.Hic static method) (fanc.hic.LegacyHic static method) (fanc.matrix.RegionMatrixContainer static method) (fanc.matrix.RegionMatrixTable static method) (fanc.matrix.RegionPairsContainer static method) (fanc.matrix.RegionPairsTable static method) (fanc.pairs.ReadPairs static method) (fanc.peaks.PeakInfo static method) (fanc.peaks.RaoPeakInfo static method) (fanc.regions.RegionsTable static method) bin_size() (fanc.architecture.comparisons.ComparisonMatrix property) (fanc.architecture.comparisons.ComparisonRegions property) (fanc.architecture.comparisons.ComparisonScores property) (fanc.architecture.comparisons.DifferenceMatrix property) (fanc.architecture.comparisons.DifferenceRegions property) (fanc.architecture.comparisons.DifferenceScores property) (fanc.architecture.comparisons.FoldChangeMatrix property) (fanc.architecture.comparisons.FoldChangeRegions property) (fanc.architecture.comparisons.FoldChangeScores property) (fanc.architecture.compartments.ABCompartmentMatrix property) (fanc.architecture.domains.Boundaries property) (fanc.architecture.domains.DirectionalityIndex property) (fanc.architecture.domains.DirectionalityIndexes property) (fanc.architecture.domains.InsulationScore property) (fanc.architecture.domains.InsulationScores property) (fanc.architecture.domains.RegionMultiScoreTable property) (fanc.architecture.domains.RegionScoreParameterTable property) (fanc.architecture.domains.RegionScoreTable property) (fanc.compatibility.cooler.CoolerHic property) (fanc.compatibility.juicer.JuicerHic property) (fanc.hic.Hic property) (fanc.hic.LegacyHic property) (fanc.matrix.RegionMatrixContainer property) (fanc.matrix.RegionMatrixTable property) (fanc.matrix.RegionPairsTable property) (fanc.pairs.ReadPairs property) (fanc.peaks.PeakInfo property) (fanc.peaks.RaoPeakInfo property) (fanc.regions.RegionsTable property)

binned_regions() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method) bins() (fanc.compatibility.cooler.CoolerHic method) bins_to_distance() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method) binsize() (fanc.compatibility.cooler.CoolerHic property) Boundaries (class in fanc.architecture.domains) Boundaries.ChromosomeDescription (class in fanc.architecture.domains) Boundaries.RegionDescription (class in fanc.architecture.domains) bowtie2_index (fanc.map.Bowtie2Mapper attribute) (fanc.map.SimpleBowtie2Mapper attribute) Bowtie2Mapper (class in fanc.map) bwa_index (fanc.map.BwaMapper attribute) (fanc.map.SimpleBwaMapper attribute) BwaMapper (class in fanc.map) BwaMemQualityFilter (class in fanc.pairs) BwaMemUniquenessFilter (class in fanc.pairs) byteswap() (fanc.matrix.RegionMatrix method)

C

C_CONTIGUOUS (fanc.matrix.RegionMatrix attribute) call_peaks() (fanc.peaks.RaoPeakCaller method) CARRAY (fanc.matrix.RegionMatrix attribute) center() (fanc.compatibility.cooler.LazyCoolerRegion property) (fanc.pairs.LazyFragment property) (fanc.regions.LazyGenomicRegion property) choose() (fanc.matrix.RegionMatrix method) chromnames() (fanc.compatibility.cooler.CoolerHic property) Chromosome (class in fanc.regions) chromosome (fanc.pairs.LazyFragment attribute) (fanc.pairs.MinimalRead attribute) chromosome_bins() (fanc.architecture.comparisons.ComparisonMatrix property) (fanc.architecture.comparisons.ComparisonRegions property) (fanc.architecture.comparisons.ComparisonScores property) (fanc.architecture.comparisons.DifferenceMatrix property) (fanc.architecture.comparisons.DifferenceRegions property) (fanc.architecture.comparisons.DifferenceScores property) (fanc.architecture.comparisons.FoldChangeMatrix property) (fanc.architecture.comparisons.FoldChangeRegions property) (fanc.architecture.comparisons.FoldChangeScores property) (fanc.architecture.compartments.ABCompartmentMatrix property) (fanc.architecture.domains.Boundaries property) (fanc.architecture.domains.DirectionalityIndex property) (fanc.architecture.domains.DirectionalityIndexes property) (fanc.architecture.domains.InsulationScore property) (fanc.architecture.domains.InsulationScores property) (fanc.architecture.domains.RegionMultiScoreTable property) (fanc.architecture.domains.RegionScoreParameterTable property) (fanc.architecture.domains.RegionScoreTable property) (fanc.compatibility.cooler.CoolerHic property) (fanc.compatibility.juicer.JuicerHic property) (fanc.hic.Hic property) (fanc.hic.LegacyHic property) (fanc.matrix.RegionMatrixContainer property) (fanc.matrix.RegionMatrixTable property) (fanc.matrix.RegionPairsTable property) (fanc.pairs.ReadPairs property) (fanc.peaks.PeakInfo property) (fanc.peaks.RaoPeakInfo property) (fanc.regions.RegionsTable property) chromosome_lengths() (fanc.architecture.comparisons.ComparisonMatrix property) (fanc.architecture.comparisons.ComparisonRegions property) (fanc.architecture.comparisons.ComparisonScores property) (fanc.architecture.comparisons.DifferenceMatrix property) (fanc.architecture.comparisons.DifferenceRegions property) (fanc.architecture.comparisons.DifferenceScores property) (fanc.architecture.comparisons.FoldChangeMatrix property) (fanc.architecture.comparisons.FoldChangeRegions property) (fanc.architecture.comparisons.FoldChangeScores property) (fanc.architecture.compartments.ABCompartmentMatrix property) (fanc.architecture.domains.Boundaries property) (fanc.architecture.domains.DirectionalityIndex property) (fanc.architecture.domains.DirectionalityIndexes property) (fanc.architecture.domains.InsulationScore property) (fanc.architecture.domains.InsulationScores property) (fanc.architecture.domains.RegionMultiScoreTable property) (fanc.architecture.domains.RegionScoreParameterTable property) (fanc.architecture.domains.RegionScoreTable property) (fanc.compatibility.cooler.CoolerHic property) (fanc.compatibility.juicer.JuicerHic property) (fanc.hic.Hic property) (fanc.hic.LegacyHic property) (fanc.matrix.RegionMatrixContainer property) (fanc.matrix.RegionMatrixTable property) (fanc.matrix.RegionPairsContainer property) (fanc.matrix.RegionPairsTable property) (fanc.pairs.ReadPairs property) (fanc.peaks.PeakInfo property) (fanc.peaks.RaoPeakInfo property) (fanc.regions.RegionsTable property) chromosomes() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.Genome method) (fanc.regions.RegionsTable method)

chroms() (fanc.compatibility.cooler.CoolerHic method) chromsizes() (fanc.compatibility.cooler.CoolerHic property) clip() (fanc.matrix.RegionMatrix method) close() (fanc.architecture.aggregate.AggregateMatrix method) (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.map.Bowtie2Mapper method) (fanc.map.BwaMapper method) (fanc.map.SimpleBowtie2Mapper method) (fanc.map.SimpleBwaMapper method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.Genome method) (fanc.regions.RegionsTable method) col_regions (fanc.matrix.RegionMatrix attribute) compare() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) ComparisonMatrix (class in fanc.architecture.comparisons) ComparisonMatrix.ChromosomeDescription (class in fanc.architecture.comparisons) ComparisonMatrix.MaskDescription (class in fanc.architecture.comparisons) ComparisonMatrix.RegionDescription (class in fanc.architecture.comparisons) ComparisonRegions (class in fanc.architecture.comparisons) ComparisonRegions.ChromosomeDescription (class in fanc.architecture.comparisons) ComparisonRegions.RegionDescription (class in fanc.architecture.comparisons) ComparisonScores (class in fanc.architecture.comparisons) ComparisonScores.ChromosomeDescription (class in fanc.architecture.comparisons) ComparisonScores.RegionDescription (class in fanc.architecture.comparisons) components() (fanc.architecture.aggregate.AggregateMatrix method) compress() (fanc.matrix.RegionMatrix method) compressed() (fanc.matrix.RegionMatrix method) conj() (fanc.matrix.RegionMatrix method) conjugate() (fanc.matrix.RegionMatrix method) contains() (fanc.compatibility.cooler.LazyCoolerRegion method) (fanc.pairs.LazyFragment method) (fanc.regions.LazyGenomicRegion method) ContaminantFilter (class in fanc.pairs) CoolerHic (class in fanc.compatibility.cooler) copy() (fanc.compatibility.cooler.LazyCoolerRegion method) (fanc.matrix.RegionMatrix method) (fanc.pairs.LazyFragment method) (fanc.regions.LazyGenomicRegion method) count() (fanc.matrix.RegionMatrix method) ctypes (fanc.matrix.RegionMatrix attribute) cumprod() (fanc.matrix.RegionMatrix method) cumsum() (fanc.matrix.RegionMatrix method)

D

data() (fanc.matrix.RegionMatrix property) diagonal() (fanc.matrix.RegionMatrix method) DiagonalFilter (class in fanc.hic) DifferenceMatrix (class in fanc.architecture.comparisons) DifferenceMatrix.ChromosomeDescription (class in fanc.architecture.comparisons) DifferenceMatrix.MaskDescription (class in fanc.architecture.comparisons) DifferenceMatrix.RegionDescription (class in fanc.architecture.comparisons) DifferenceRegions (class in fanc.architecture.comparisons) DifferenceRegions.ChromosomeDescription (class in fanc.architecture.comparisons) DifferenceRegions.RegionDescription (class in fanc.architecture.comparisons) DifferenceScores (class in fanc.architecture.comparisons) DifferenceScores.ChromosomeDescription (class in fanc.architecture.comparisons) DifferenceScores.RegionDescription (class in fanc.architecture.comparisons) DirectionalityIndex (class in fanc.architecture.domains) DirectionalityIndex.ChromosomeDescription (class in fanc.architecture.domains) DirectionalityIndex.RegionDescription (class in fanc.architecture.domains) DirectionalityIndexes (class in fanc.architecture.domains) DirectionalityIndexes.ChromosomeDescription (class in fanc.architecture.domains) DirectionalityIndexes.RegionDescription (class in fanc.architecture.domains) distance_decay_plot() (in module fanc.plotting) distance_to_bins() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method)

DistancePeakFilter (class in fanc.peaks) domains() (fanc.architecture.compartments.ABCompartmentMatrix method) dot() (fanc.matrix.RegionMatrix method) downsample() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) dtype() (fanc.matrix.RegionMatrix property) dump() (fanc.matrix.RegionMatrix method) dumps() (fanc.matrix.RegionMatrix method)

E

e_d() (fanc.peaks.RaoPeakCaller static method) e_h() (fanc.peaks.RaoPeakCaller static method) e_ll() (fanc.peaks.RaoPeakCaller static method) e_v() (fanc.peaks.RaoPeakCaller static method) Edge (class in fanc.matrix) edge_data() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) edge_subset() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) edges() (fanc.architecture.comparisons.ComparisonMatrix property) (fanc.architecture.comparisons.DifferenceMatrix property) (fanc.architecture.comparisons.FoldChangeMatrix property) (fanc.architecture.compartments.ABCompartmentMatrix property) (fanc.compatibility.cooler.CoolerHic property) (fanc.compatibility.juicer.JuicerHic property) (fanc.hic.Hic property) (fanc.hic.LegacyHic property) (fanc.matrix.RegionMatrixContainer property) (fanc.matrix.RegionMatrixTable property) (fanc.matrix.RegionPairsContainer property) (fanc.matrix.RegionPairsTable property) (fanc.pairs.ReadPairs property) (fanc.peaks.PeakInfo property) (fanc.peaks.RaoPeakInfo property)

edges_dict() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) eigenvector() (fanc.architecture.compartments.ABCompartmentMatrix method) end (fanc.pairs.LazyFragment attribute) enrichment_profile() (fanc.architecture.compartments.ABCompartmentMatrix method) EnrichmentPeakFilter (class in fanc.peaks) example_data (in module fanc.plotting) expand() (fanc.compatibility.cooler.LazyCoolerRegion method) (fanc.pairs.LazyFragment method) (fanc.regions.LazyGenomicRegion method) expected_values() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) expected_values_and_marginals() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) extent() (fanc.compatibility.cooler.CoolerHic method)

F

F_CONTIGUOUS (fanc.matrix.RegionMatrix attribute) fanc.__init__ (module) fanc.architecture.aggregate (module) fanc.architecture.comparisons (module) fanc.architecture.compartments (module) fanc.architecture.domains (module) fanc.compatibility.cooler (module) fanc.compatibility.juicer (module) fanc.hic (module) fanc.map (module) fanc.matrix (module) fanc.pairs (module) fanc.peaks (module) fanc.plotting (module) fanc.regions (module) fanc.tools.load (module) FARRAY (fanc.matrix.RegionMatrix attribute) FdrPeakFilter (class in fanc.peaks) FdrSumFilter (class in fanc.peaks) FeatureLayerPlot (class in fanc.plotting) fill() (fanc.matrix.RegionMatrix method) fill_value() (fanc.matrix.RegionMatrix property) filled() (fanc.matrix.RegionMatrix method) filter() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) filter_diagonal() (fanc.hic.Hic method) (fanc.hic.LegacyHic method) filter_enrichment() (fanc.peaks.RaoPeakInfo method) filter_fdr() (fanc.peaks.RaoPeakInfo method) filter_inward() (fanc.pairs.ReadPairs method) filter_ligation_products() (fanc.pairs.ReadPairs method) filter_low_coverage_regions() (fanc.hic.Hic method) (fanc.hic.LegacyHic method) filter_mappability() (fanc.peaks.RaoPeakInfo method) filter_multi_mapping() (fanc.pairs.SamBamReadPairGenerator method) filter_observed() (fanc.peaks.RaoPeakInfo method) filter_outward() (fanc.pairs.ReadPairs method) filter_pcr_duplicates() (fanc.pairs.ReadPairs method) filter_quality() (fanc.pairs.SamBamReadPairGenerator method) filter_rao() (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) filter_re_dist() (fanc.pairs.ReadPairs method) filter_self_ligated() (fanc.pairs.ReadPairs method) filter_statistics() (fanc.pairs.ReadPairs method) filter_unmapped() (fanc.pairs.SamBamReadPairGenerator method) find_chunk() (fanc.peaks.RaoPeakCaller static method) find_region() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method)

five_prime() (fanc.compatibility.cooler.LazyCoolerRegion property) (fanc.pairs.LazyFragment property) (fanc.regions.LazyGenomicRegion property) fix_chromosome() (fanc.compatibility.cooler.LazyCoolerRegion method) (fanc.pairs.LazyFragment method) (fanc.regions.LazyGenomicRegion method) flag (fanc.pairs.MinimalRead attribute) flags (fanc.matrix.RegionMatrix attribute) flat() (fanc.matrix.RegionMatrix property) flatten() (fanc.matrix.RegionMatrix method) flush() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method) FNC (fanc.matrix.RegionMatrix attribute) FoldChangeMatrix (class in fanc.architecture.comparisons) FoldChangeMatrix.ChromosomeDescription (class in fanc.architecture.comparisons) FoldChangeMatrix.MaskDescription (class in fanc.architecture.comparisons) FoldChangeMatrix.RegionDescription (class in fanc.architecture.comparisons) FoldChangeRegions (class in fanc.architecture.comparisons) FoldChangeRegions.ChromosomeDescription (class in fanc.architecture.comparisons) FoldChangeRegions.RegionDescription (class in fanc.architecture.comparisons) FoldChangeScores (class in fanc.architecture.comparisons) FoldChangeScores.ChromosomeDescription (class in fanc.architecture.comparisons) FoldChangeScores.RegionDescription (class in fanc.architecture.comparisons) FORC (fanc.matrix.RegionMatrix attribute) FourDNucleomePairGenerator (class in fanc.pairs) fragment (fanc.pairs.FragmentRead attribute) (fanc.pairs.LazyFragmentRead attribute) FragmentRead (class in fanc.pairs) FragmentReadPair (class in fanc.pairs) FragmentReadPairFilter (class in fanc.pairs) from_center() (fanc.architecture.aggregate.AggregateMatrix class method) from_center_pairs() (fanc.architecture.aggregate.AggregateMatrix class method) from_fasta() (fanc.regions.Chromosome class method) from_folder() (fanc.regions.Genome class method) from_hic() (fanc.architecture.compartments.ABCompartmentMatrix class method) (fanc.architecture.domains.DirectionalityIndexes class method) (fanc.architecture.domains.InsulationScores class method) from_insulation_score() (fanc.architecture.domains.Boundaries class method) from_matrices() (fanc.architecture.comparisons.ComparisonMatrix class method) (fanc.architecture.comparisons.DifferenceMatrix class method) (fanc.architecture.comparisons.FoldChangeMatrix class method) from_regions() (fanc.architecture.aggregate.AggregateMatrix class method) (fanc.architecture.comparisons.ComparisonRegions class method) (fanc.architecture.comparisons.DifferenceRegions class method) (fanc.architecture.comparisons.FoldChangeRegions class method) from_scores() (fanc.architecture.comparisons.ComparisonScores class method) (fanc.architecture.comparisons.DifferenceScores class method) (fanc.architecture.comparisons.FoldChangeScores class method) from_string() (fanc.compatibility.cooler.LazyCoolerRegion class method) (fanc.pairs.LazyFragment class method) (fanc.regions.Genome class method) (fanc.regions.LazyGenomicRegion class method)

G

GenePlot (class in fanc.plotting) generate_pairs() (in module fanc.pairs) generate_pairs_split() (in module fanc.pairs) Genome (class in fanc.regions) Genome.ChromosomeDefinition (class in fanc.regions) genome_regions() (in module fanc.regions) GenomicDataFramePlot (class in fanc.plotting) GenomicFeaturePlot (class in fanc.plotting) GenomicFeatureScorePlot (class in fanc.plotting) GenomicFigure (class in fanc.plotting) GenomicRegionsPlot (class in fanc.plotting) GenomicVectorArrayPlot (class in fanc.plotting) get_edge() (fanc.pairs.ReadPairs method) get_fill_value() (fanc.matrix.RegionMatrix method) get_gap_size() (fanc.pairs.FragmentReadPair method) get_imag() (fanc.matrix.RegionMatrix method) get_ligation_structure_biases() (fanc.pairs.ReadPairs method) get_mask() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method)

get_masks() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) get_real() (fanc.matrix.RegionMatrix method) get_regions() (fanc.regions.Genome method) get_restriction_sites() (fanc.regions.Chromosome method) getfield() (fanc.matrix.RegionMatrix method)

H

harden_mask() (fanc.matrix.RegionMatrix method) hardmask() (fanc.matrix.RegionMatrix property) Hic (class in fanc.hic) Hic.ChromosomeDescription (class in fanc.hic) Hic.MaskDescription (class in fanc.hic) Hic.RegionDescription (class in fanc.hic)

hic_pca() (in module fanc.architecture.comparisons) HicComparisonPlot2D (in module fanc.plotting) HicEdgeFilter (class in fanc.hic) HicPeakPlot (class in fanc.plotting) HicProPairGenerator (class in fanc.pairs) HicSlicePlot (class in fanc.plotting) HighlightAnnotation (class in fanc.plotting)

I

ice_balancing() (in module fanc.hic) ids() (fanc.matrix.RegionMatrix method) imag() (fanc.matrix.RegionMatrix property) info() (fanc.compatibility.cooler.CoolerHic property) InsulationScore (class in fanc.architecture.domains) InsulationScore.ChromosomeDescription (class in fanc.architecture.domains) InsulationScore.RegionDescription (class in fanc.architecture.domains) InsulationScores (class in fanc.architecture.domains) InsulationScores.ChromosomeDescription (class in fanc.architecture.domains) InsulationScores.RegionDescription (class in fanc.architecture.domains) intervals() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method)

InwardPairsFilter (class in fanc.pairs) is_forward() (fanc.compatibility.cooler.LazyCoolerRegion method) (fanc.pairs.LazyFragment method) (fanc.regions.LazyGenomicRegion method) is_generating_pairs() (fanc.pairs.Monitor method) is_inward_pair() (fanc.pairs.FragmentReadPair method) is_outward_pair() (fanc.pairs.FragmentReadPair method) is_reverse() (fanc.compatibility.cooler.LazyCoolerRegion method) (fanc.pairs.LazyFragment method) (fanc.regions.LazyGenomicRegion method) is_same_chromosome() (fanc.pairs.FragmentReadPair method) is_same_fragment() (fanc.pairs.FragmentReadPair method) is_same_pair() (fanc.pairs.FragmentReadPair method) iscontiguous() (fanc.matrix.RegionMatrix method) item() (fanc.matrix.RegionMatrix method) itemset() (fanc.matrix.RegionMatrix method) itemsize (fanc.matrix.RegionMatrix attribute) iterative_mapping() (in module fanc.map) ix (fanc.pairs.LazyFragment attribute) ix() (fanc.regions.LazyGenomicRegion property)

J

JuicerHic (class in fanc.compatibility.juicer)

L

LazyCoolerRegion (class in fanc.compatibility.cooler) LazyEdge (class in fanc.matrix) LazyFragment (class in fanc.pairs) LazyFragmentRead (class in fanc.pairs) LazyGenomicRegion (class in fanc.regions) LazyPeak (class in fanc.peaks) LegacyHic (class in fanc.hic) LegacyHic.ChromosomeDescription (class in fanc.hic) LegacyHic.MaskDescription (class in fanc.hic)

LegacyHic.RegionDescription (class in fanc.hic) length (fanc.regions.Chromosome attribute) LimitGroup (class in fanc.plotting) LinePlot (class in fanc.plotting) ll_sum() (fanc.peaks.RaoPeakCaller static method) load() (in module fanc.tools.load) load_from_hic() (fanc.hic.Hic method) (fanc.hic.LegacyHic method) LowCoverageFilter (class in fanc.hic)

M

map() (fanc.map.Bowtie2Mapper method) (fanc.map.BwaMapper method) (fanc.map.SimpleBowtie2Mapper method) (fanc.map.SimpleBwaMapper method) MappabilityPeakFilter (class in fanc.peaks) mappable() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) marginals() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) mask() (fanc.matrix.RegionMatrix property) matrix() (fanc.architecture.aggregate.AggregateMatrix method) (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method)

max() (fanc.matrix.RegionMatrix method) mean() (fanc.matrix.RegionMatrix method) merge() (fanc.architecture.comparisons.ComparisonMatrix class method) (fanc.architecture.comparisons.DifferenceMatrix class method) (fanc.architecture.comparisons.FoldChangeMatrix class method) (fanc.architecture.compartments.ABCompartmentMatrix class method) (fanc.compatibility.cooler.CoolerHic class method) (fanc.compatibility.juicer.JuicerHic class method) (fanc.hic.Hic class method) (fanc.hic.LegacyHic class method) (fanc.matrix.RegionMatrixContainer class method) (fanc.matrix.RegionMatrixTable class method) (fanc.matrix.RegionPairsContainer class method) (fanc.matrix.RegionPairsTable class method) (fanc.pairs.ReadPairs class method) (fanc.peaks.PeakInfo class method) (fanc.peaks.RaoPeakInfo class method) merged_peaks() (fanc.peaks.RaoPeakInfo method) min() (fanc.matrix.RegionMatrix method) min_quality (fanc.map.Bowtie2Mapper attribute) (fanc.map.BwaMapper attribute) (fanc.map.SimpleBwaMapper attribute) mini() (fanc.matrix.RegionMatrix method) MinimalRead (class in fanc.pairs) MirrorMatrixPlot (class in fanc.plotting) Monitor (class in fanc.pairs) MutableLazyEdge (class in fanc.matrix)

N

name (fanc.regions.Chromosome attribute) nbytes (fanc.matrix.RegionMatrix attribute)

ndim (fanc.matrix.RegionMatrix attribute) newbyteorder() (fanc.matrix.RegionMatrix method) nonzero() (fanc.matrix.RegionMatrix method)

O

ObservedPeakFilter (class in fanc.peaks) offset() (fanc.compatibility.cooler.CoolerHic method) open() (fanc.compatibility.cooler.CoolerHic method) OutwardPairsFilter (class in fanc.pairs) overlap() (fanc.compatibility.cooler.LazyCoolerRegion method) (fanc.pairs.LazyFragment method) (fanc.regions.LazyGenomicRegion method)

overlap_peaks() (in module fanc.peaks) overlaps() (fanc.compatibility.cooler.LazyCoolerRegion method) (fanc.pairs.LazyFragment method) (fanc.regions.LazyGenomicRegion method) OWNDATA (fanc.matrix.RegionMatrix attribute)

P

PairedSamBamReadPairGenerator (class in fanc.pairs) pairs() (fanc.pairs.ReadPairs method) pairs_by_chromosomes() (fanc.pairs.ReadPairs method) partition() (fanc.matrix.RegionMatrix method) pca_plot() (in module fanc.plotting) PCRDuplicateFilter (class in fanc.pairs) Peak (class in fanc.peaks) PeakFilter (class in fanc.peaks) PeakInfo (class in fanc.peaks) PeakInfo.ChromosomeDescription (class in fanc.peaks) PeakInfo.MaskDescription (class in fanc.peaks) PeakInfo.RegionDescription (class in fanc.peaks) pixels() (fanc.compatibility.cooler.CoolerHic method) plot() (fanc.plotting.GenomicFigure method) pos (fanc.pairs.MinimalRead attribute) position (fanc.pairs.FragmentRead attribute) (fanc.pairs.LazyFragmentRead attribute) (fanc.pairs.MinimalRead attribute)

possible_contacts() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) prod() (fanc.matrix.RegionMatrix method) product() (fanc.matrix.RegionMatrix method) ptp() (fanc.matrix.RegionMatrix method) put() (fanc.matrix.RegionMatrix method)

Q

QualityFilter (class in fanc.pairs)

R

RaoMergedPeakFilter (class in fanc.peaks) RaoPeakCaller (class in fanc.peaks) RaoPeakFilter (class in fanc.peaks) RaoPeakInfo (class in fanc.peaks) RaoPeakInfo.ChromosomeDescription (class in fanc.peaks) RaoPeakInfo.MaskDescription (class in fanc.peaks) RaoPeakInfo.RegionDescription (class in fanc.peaks) ravel() (fanc.matrix.RegionMatrix method) re_distance() (fanc.pairs.FragmentRead method) (fanc.pairs.LazyFragmentRead method) ReadFilter (class in fanc.pairs) ReadPairGenerator (class in fanc.pairs) ReadPairs (class in fanc.pairs) ReadPairs.ChromosomeDescription (class in fanc.pairs) ReadPairs.MaskDescription (class in fanc.pairs) ReadPairs.RegionDescription (class in fanc.pairs) real() (fanc.matrix.RegionMatrix property) recordmask() (fanc.matrix.RegionMatrix property) ReDistanceFilter (class in fanc.pairs) reference_name (fanc.pairs.MinimalRead attribute) region_bins() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method) region_data() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method) region_intervals() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method) region_pairs() (fanc.architecture.aggregate.AggregateMatrix method) region_subset() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method) RegionMatrix (class in fanc.matrix) RegionMatrixContainer (class in fanc.matrix) RegionMatrixTable (class in fanc.matrix) RegionMatrixTable.ChromosomeDescription (class in fanc.matrix)

RegionMatrixTable.MaskDescription (class in fanc.matrix) RegionMatrixTable.RegionDescription (class in fanc.matrix) RegionMultiScoreTable (class in fanc.architecture.domains) RegionMultiScoreTable.ChromosomeDescription (class in fanc.architecture.domains) RegionMultiScoreTable.RegionDescription (class in fanc.architecture.domains) RegionPairsContainer (class in fanc.matrix) RegionPairsTable (class in fanc.matrix) RegionPairsTable.ChromosomeDescription (class in fanc.matrix) RegionPairsTable.MaskDescription (class in fanc.matrix) RegionPairsTable.RegionDescription (class in fanc.matrix) regions() (fanc.architecture.comparisons.ComparisonMatrix property) (fanc.architecture.comparisons.ComparisonRegions property) (fanc.architecture.comparisons.ComparisonScores property) (fanc.architecture.comparisons.DifferenceMatrix property) (fanc.architecture.comparisons.DifferenceRegions property) (fanc.architecture.comparisons.DifferenceScores property) (fanc.architecture.comparisons.FoldChangeMatrix property) (fanc.architecture.comparisons.FoldChangeRegions property) (fanc.architecture.comparisons.FoldChangeScores property) (fanc.architecture.compartments.ABCompartmentMatrix property) (fanc.architecture.domains.Boundaries property) (fanc.architecture.domains.DirectionalityIndex property) (fanc.architecture.domains.DirectionalityIndexes property) (fanc.architecture.domains.InsulationScore property) (fanc.architecture.domains.InsulationScores property) (fanc.architecture.domains.RegionMultiScoreTable property) (fanc.architecture.domains.RegionScoreParameterTable property) (fanc.architecture.domains.RegionScoreTable property) (fanc.compatibility.cooler.CoolerHic property) (fanc.compatibility.juicer.JuicerHic property) (fanc.hic.Hic property) (fanc.hic.LegacyHic property) (fanc.matrix.RegionMatrixContainer property) (fanc.matrix.RegionMatrixTable property) (fanc.matrix.RegionPairsContainer property) (fanc.matrix.RegionPairsTable property) (fanc.pairs.ReadPairs property) (fanc.peaks.PeakInfo property) (fanc.peaks.RaoPeakInfo property) (fanc.regions.RegionsTable property) regions_and_edges() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) regions_and_matrix_entries() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) regions_dict() (fanc.architecture.comparisons.ComparisonMatrix property) (fanc.architecture.comparisons.ComparisonRegions property) (fanc.architecture.comparisons.ComparisonScores property) (fanc.architecture.comparisons.DifferenceMatrix property) (fanc.architecture.comparisons.DifferenceRegions property) (fanc.architecture.comparisons.DifferenceScores property) (fanc.architecture.comparisons.FoldChangeMatrix property) (fanc.architecture.comparisons.FoldChangeRegions property) (fanc.architecture.comparisons.FoldChangeScores property) (fanc.architecture.compartments.ABCompartmentMatrix property) (fanc.architecture.domains.Boundaries property) (fanc.architecture.domains.DirectionalityIndex property) (fanc.architecture.domains.DirectionalityIndexes property) (fanc.architecture.domains.InsulationScore property) (fanc.architecture.domains.InsulationScores property) (fanc.architecture.domains.RegionMultiScoreTable property) (fanc.architecture.domains.RegionScoreParameterTable property) (fanc.architecture.domains.RegionScoreTable property) (fanc.compatibility.cooler.CoolerHic property) (fanc.compatibility.juicer.JuicerHic property) (fanc.hic.Hic property) (fanc.hic.LegacyHic property) (fanc.matrix.RegionMatrixContainer property) (fanc.matrix.RegionMatrixTable property) (fanc.matrix.RegionPairsContainer property) (fanc.matrix.RegionPairsTable property) (fanc.pairs.ReadPairs property) (fanc.peaks.PeakInfo property) (fanc.peaks.RaoPeakInfo property) (fanc.regions.RegionsTable property) regions_identical() (fanc.architecture.comparisons.ComparisonMatrix static method) (fanc.architecture.comparisons.DifferenceMatrix static method) (fanc.architecture.comparisons.FoldChangeMatrix static method) (fanc.architecture.compartments.ABCompartmentMatrix static method) (fanc.compatibility.cooler.CoolerHic static method) (fanc.compatibility.juicer.JuicerHic static method) (fanc.hic.Hic static method) (fanc.hic.LegacyHic static method) (fanc.matrix.RegionMatrixContainer static method) (fanc.matrix.RegionMatrixTable static method) (fanc.matrix.RegionPairsContainer static method) (fanc.matrix.RegionPairsTable static method) (fanc.pairs.ReadPairs static method) (fanc.peaks.PeakInfo static method) (fanc.peaks.RaoPeakInfo static method) RegionScoreParameterTable (class in fanc.architecture.domains) RegionScoreParameterTable.ChromosomeDescription (class in fanc.architecture.domains) RegionScoreParameterTable.RegionDescription (class in fanc.architecture.domains) RegionScoreTable (class in fanc.architecture.domains) RegionScoreTable.ChromosomeDescription (class in fanc.architecture.domains) RegionScoreTable.RegionDescription (class in fanc.architecture.domains) RegionsTable (class in fanc.regions) RegionsTable.ChromosomeDescription (class in fanc.regions) RegionsTable.RegionDescription (class in fanc.regions) repeat() (fanc.matrix.RegionMatrix method) reshape() (fanc.matrix.RegionMatrix method) resize() (fanc.matrix.RegionMatrix method) resolve_chimeric() (fanc.pairs.PairedSamBamReadPairGenerator static method) resubmit() (fanc.map.Bowtie2Mapper method) (fanc.map.BwaMapper method) (fanc.map.SimpleBowtie2Mapper method) (fanc.map.SimpleBwaMapper method) round() (fanc.matrix.RegionMatrix method) row_regions (fanc.matrix.RegionMatrix attribute) run_queued_filters() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method)

S

SamBamReadPairGenerator (class in fanc.pairs) scaling_factor() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) score_regions() (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionScoreParameterTable method) scores() (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) searchsorted() (fanc.matrix.RegionMatrix method) SelfLigationFilter (class in fanc.pairs) sequence (fanc.regions.Chromosome attribute) set_attribute() (fanc.compatibility.cooler.LazyCoolerRegion method) (fanc.pairs.LazyFragment method) (fanc.regions.LazyGenomicRegion method) set_generating_pairs() (fanc.pairs.Monitor method) set_hic_object() (fanc.hic.DiagonalFilter method) (fanc.hic.HicEdgeFilter method) (fanc.hic.LowCoverageFilter method) setfield() (fanc.matrix.RegionMatrix method) setflags() (fanc.matrix.RegionMatrix method) shape() (fanc.matrix.RegionMatrix property) sharedmask() (fanc.matrix.RegionMatrix property) shrink_mask() (fanc.matrix.RegionMatrix method) SimpleBowtie2Mapper (class in fanc.map) SimpleBwaMapper (class in fanc.map) sink (fanc.matrix.Edge attribute) (fanc.matrix.LazyEdge attribute)

sink_node (fanc.matrix.Edge attribute) (fanc.matrix.LazyEdge attribute) size (fanc.matrix.RegionMatrix attribute) soften_mask() (fanc.matrix.RegionMatrix method) sort() (fanc.matrix.RegionMatrix method) source (fanc.matrix.Edge attribute) (fanc.matrix.LazyEdge attribute) source_node (fanc.matrix.Edge attribute) (fanc.matrix.LazyEdge attribute) SplitMatrixPlot (class in fanc.plotting) sqrt_vanilla_coverage_norm() (in module fanc.hic) SquareMatrixPlot (class in fanc.plotting) squeeze() (fanc.matrix.RegionMatrix method) start (fanc.pairs.LazyFragment attribute) stats() (fanc.pairs.FourDNucleomePairGenerator method) (fanc.pairs.HicProPairGenerator method) (fanc.pairs.PairedSamBamReadPairGenerator method) (fanc.pairs.ReadPairGenerator method) (fanc.pairs.SamBamReadPairGenerator method) (fanc.pairs.TxtReadPairGenerator method) std() (fanc.matrix.RegionMatrix method) storage_mode() (fanc.compatibility.cooler.CoolerHic property) strand (fanc.pairs.FragmentRead attribute) (fanc.pairs.LazyFragment attribute) (fanc.pairs.LazyFragmentRead attribute) (fanc.pairs.MinimalRead attribute) strand() (fanc.regions.LazyGenomicRegion property) strand_string() (fanc.compatibility.cooler.LazyCoolerRegion property) (fanc.pairs.LazyFragment property) (fanc.regions.LazyGenomicRegion property) strides (fanc.matrix.RegionMatrix attribute) style_ticks_whitegrid (in module fanc.plotting) sub_sequence() (fanc.regions.Genome method) subset() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) sum() (fanc.matrix.RegionMatrix method) swapaxes() (fanc.matrix.RegionMatrix method) SymmetricNorm (class in fanc.plotting)

T

take() (fanc.matrix.RegionMatrix method) threads (fanc.map.Bowtie2Mapper attribute) (fanc.map.BwaMapper attribute) (fanc.map.SimpleBowtie2Mapper attribute) (fanc.map.SimpleBwaMapper attribute) three_prime() (fanc.compatibility.cooler.LazyCoolerRegion property) (fanc.pairs.LazyFragment property) (fanc.regions.LazyGenomicRegion property) to_bed() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method) to_bigwig() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method)

to_cooler() (in module fanc.compatibility.cooler) to_gff() (fanc.architecture.comparisons.ComparisonMatrix method) (fanc.architecture.comparisons.ComparisonRegions method) (fanc.architecture.comparisons.ComparisonScores method) (fanc.architecture.comparisons.DifferenceMatrix method) (fanc.architecture.comparisons.DifferenceRegions method) (fanc.architecture.comparisons.DifferenceScores method) (fanc.architecture.comparisons.FoldChangeMatrix method) (fanc.architecture.comparisons.FoldChangeRegions method) (fanc.architecture.comparisons.FoldChangeScores method) (fanc.architecture.compartments.ABCompartmentMatrix method) (fanc.architecture.domains.Boundaries method) (fanc.architecture.domains.DirectionalityIndex method) (fanc.architecture.domains.DirectionalityIndexes method) (fanc.architecture.domains.InsulationScore method) (fanc.architecture.domains.InsulationScores method) (fanc.architecture.domains.RegionMultiScoreTable method) (fanc.architecture.domains.RegionScoreParameterTable method) (fanc.architecture.domains.RegionScoreTable method) (fanc.compatibility.cooler.CoolerHic method) (fanc.compatibility.juicer.JuicerHic method) (fanc.hic.Hic method) (fanc.hic.LegacyHic method) (fanc.matrix.RegionMatrixContainer method) (fanc.matrix.RegionMatrixTable method) (fanc.matrix.RegionPairsContainer method) (fanc.matrix.RegionPairsTable method) (fanc.pairs.ReadPairs method) (fanc.peaks.PeakInfo method) (fanc.peaks.RaoPeakInfo method) (fanc.regions.RegionsTable method) to_hic() (fanc.pairs.ReadPairs method) to_string() (fanc.compatibility.cooler.LazyCoolerRegion method) (fanc.pairs.LazyFragment method) (fanc.regions.LazyGenomicRegion method) tobytes() (fanc.matrix.RegionMatrix method) tofile() (fanc.matrix.RegionMatrix method) toflex() (fanc.matrix.RegionMatrix method) tolist() (fanc.matrix.RegionMatrix method) torecords() (fanc.matrix.RegionMatrix method) tostring() (fanc.matrix.RegionMatrix method) trace() (fanc.matrix.RegionMatrix method) transpose() (fanc.matrix.RegionMatrix method) TriangularMatrixPlot (class in fanc.plotting) TxtReadPairGenerator (class in fanc.pairs)

U

UniquenessFilter (class in fanc.pairs) UnmappedFilter (class in fanc.pairs)

unshare_mask() (fanc.matrix.RegionMatrix method) update() (fanc.matrix.MutableLazyEdge method) UPDATEIFCOPY (fanc.matrix.RegionMatrix attribute)

V

valid() (fanc.hic.DiagonalFilter method) (fanc.hic.HicEdgeFilter method) (fanc.hic.LowCoverageFilter method) (fanc.pairs.FragmentReadPairFilter method) (fanc.pairs.InwardPairsFilter method) (fanc.pairs.OutwardPairsFilter method) (fanc.pairs.PCRDuplicateFilter method) (fanc.pairs.ReDistanceFilter method) (fanc.pairs.SelfLigationFilter method) (fanc.peaks.DistancePeakFilter method) (fanc.peaks.EnrichmentPeakFilter method) (fanc.peaks.FdrPeakFilter method) (fanc.peaks.FdrSumFilter method) (fanc.peaks.MappabilityPeakFilter method) (fanc.peaks.ObservedPeakFilter method) (fanc.peaks.PeakFilter method) (fanc.peaks.RaoMergedPeakFilter method) (fanc.peaks.RaoPeakFilter method) valid_edge() (fanc.hic.DiagonalFilter method) (fanc.hic.HicEdgeFilter method) (fanc.hic.LowCoverageFilter method) valid_pair() (fanc.pairs.InwardPairsFilter method) (fanc.pairs.PCRDuplicateFilter method) (fanc.pairs.ReDistanceFilter method) (fanc.pairs.SelfLigationFilter method)

valid_peak() (fanc.peaks.DistancePeakFilter method) (fanc.peaks.EnrichmentPeakFilter method) (fanc.peaks.FdrPeakFilter method) (fanc.peaks.FdrSumFilter method) (fanc.peaks.MappabilityPeakFilter method) (fanc.peaks.ObservedPeakFilter method) (fanc.peaks.PeakFilter method) (fanc.peaks.RaoMergedPeakFilter method) (fanc.peaks.RaoPeakFilter method) valid_read() (fanc.pairs.BwaMemQualityFilter method) (fanc.pairs.BwaMemUniquenessFilter method) (fanc.pairs.ContaminantFilter method) (fanc.pairs.QualityFilter method) (fanc.pairs.ReadFilter method) (fanc.pairs.UniquenessFilter method) (fanc.pairs.UnmappedFilter method) vanilla_coverage_norm() (in module fanc.hic) var() (fanc.matrix.RegionMatrix method) VerticalSplitPlot (in module fanc.plotting) view() (fanc.matrix.RegionMatrix method)

W

window_sizes() (fanc.architecture.domains.DirectionalityIndexes property) (fanc.architecture.domains.InsulationScores property)

WRITEABLE (fanc.matrix.RegionMatrix attribute) WRITEBACKIFCOPY (fanc.matrix.RegionMatrix attribute)