Index

_

__flag_sorted (MACS3.IO.PeakIO.RegionIO attribute)

A

add() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.IO.PeakIO.PeakIO method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) add_C() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) add_chrom_data() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) add_chrom_data_PV() (MACS3.Signal.BedGraph.bedGraphTrackI method) add_chromosome() (MACS3.Signal.ScoreTrack.ScoreTrackII method) add_loc() (MACS3.IO.PeakIO.RegionIO method) (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) (MACS3.Signal.Region.Regions method) add_loc_wo_merge() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method)

add_PeakContent() (MACS3.IO.PeakIO.PeakIO method) add_T() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) add_variant() (MACS3.Signal.PeakVariants.PeakVariants method) alternative_d (MACS3.Signal.PeakModel.PeakModel attribute) annotation (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) append_fwtrack() (MACS3.IO.Parser.BAMParser method) (MACS3.IO.Parser.GenericParser method) append_petrack() (MACS3.IO.Parser.BAMPEParser method) (MACS3.IO.Parser.BEDPEParser method) (MACS3.IO.Parser.FragParser method) apply_deltaBIC_cutoff() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) apply_func() (MACS3.Signal.BedGraph.bedGraphTrackI method) apply_GQ_cutoff() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) average_template_length (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute)

B

bai_filename (MACS3.IO.BAM.BAMaccessor attribute) BAIFile (class in MACS3.IO.BAM) baifile (MACS3.IO.BAM.BAMaccessor attribute) bam_filename (MACS3.IO.BAM.BAMaccessor attribute) BAMaccessor (class in MACS3.IO.BAM) bamfile (MACS3.IO.BAM.BAMaccessor attribute) BAMParser (class in MACS3.IO.Parser) BAMPEParser (class in MACS3.IO.Parser) barcode_dict (MACS3.Signal.PairedEndTrack.PETrackII attribute) barcodes (MACS3.Signal.PairedEndTrack.PETrackII attribute) baseline_value (MACS3.Signal.BedGraph.bedGraphTrackI attribute) (MACS3.Signal.BedGraph.bedGraphTrackII attribute) bedGraph_filename_prefix (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) bedGraphIO (class in MACS3.IO.BedGraphIO) bedGraphTrackI (class in MACS3.Signal.BedGraph) bedGraphTrackII (class in MACS3.Signal.BedGraph) BEDParser (class in MACS3.IO.Parser) BEDPEParser (class in MACS3.IO.Parser) bgzf_block_cache (MACS3.IO.BAM.BAMaccessor attribute) binomial_cdf() (in module MACS3.Signal.Prob)

binomial_cdf_inv() (in module MACS3.Signal.Prob) binomial_pdf() (in module MACS3.Signal.Prob) binomial_sf() (in module MACS3.Signal.Prob) bins (MACS3.IO.BAM.BAIFile attribute) BowtieParser (class in MACS3.IO.Parser) BroadPeakContent (class in MACS3.IO.PeakIO) BroadPeakIO (class in MACS3.IO.PeakIO) buf_size (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) buffer_size (MACS3.IO.Parser.GenericParser attribute) (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) build() (MACS3.Signal.PeakModel.PeakModel method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) build_fwtrack() (MACS3.IO.Parser.BAMParser method) (MACS3.IO.Parser.GenericParser method) build_petrack() (MACS3.IO.Parser.BAMPEParser method) (MACS3.IO.Parser.BEDPEParser method) (MACS3.IO.Parser.FragParser method) build_unitig_collection() (MACS3.Signal.RACollection.RACollection method)

C

cal_max_dup_tags() (in module MACS3.Commands.callpeak_cmd) (in module MACS3.Commands.filterdup_cmd) calculate_GQ() (in module MACS3.Signal.VariantStat) calculate_GQ_heterASsig() (in module MACS3.Signal.VariantStat) call_broadpeaks() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.CallPeakUnit.CallerFromAlignments method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) call_GT() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) call_peaks() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.CallPeakUnit.CallerFromAlignments method) (MACS3.Signal.PeakDetect.PeakDetect method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) call_variants_at_range() (in module MACS3.Commands.callvar_cmd) CallerFromAlignments (class in MACS3.Signal.CallPeakUnit) CalModel_Heter_AS() (in module MACS3.Signal.VariantStat) CalModel_Heter_noAS() (in module MACS3.Signal.VariantStat) CalModel_Homo() (in module MACS3.Signal.VariantStat)

change_normalization_method() (MACS3.Signal.ScoreTrack.ScoreTrackII method) change_score_method() (MACS3.Signal.ScoreTrack.ScoreTrackII method) check_names() (in module MACS3.Commands.callpeak_cmd) (in module MACS3.Commands.callvar_cmd) chisq_logp_e() (in module MACS3.Signal.Prob) chisq_pvalue_e() (in module MACS3.Signal.Prob) chrom (MACS3.IO.PeakIO.PeakContent attribute) chromosomes (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) close() (MACS3.IO.BAM.BAMaccessor method) (MACS3.IO.Parser.GenericParser method) CO_sorted (MACS3.IO.PeakIO.PeakIO attribute), [1] coffset_cache (MACS3.IO.BAM.BAMaccessor attribute) compute_region_tags_from_peaks() (MACS3.Signal.FixWidthTrack.FWTrack method) count_fraglengths() (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) ctrl (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) ctrl_d_s (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) ctrl_scaling_factor_s (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) cutoff_analysis() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.ScoreTrack.ScoreTrackII method)

D

d (MACS3.IO.Parser.BAMPEParser attribute) (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) (MACS3.Signal.PeakModel.PeakModel attribute) destroy() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.CallPeakUnit.CallerFromAlignments method) (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method)

diag_write() (in module MACS3.IO.OutputWriter)

E

ELANDExportParser (class in MACS3.IO.Parser) ELANDMultiParser (class in MACS3.IO.Parser) ELANDResultParser (class in MACS3.IO.Parser) enable_trackline() (MACS3.Signal.CallPeakUnit.CallerFromAlignments method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) end (MACS3.IO.PeakIO.PeakContent attribute) end_shift (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) enforce_peakyness() (in module MACS3.Signal.SignalProcessing) enforce_valleys() (in module MACS3.Signal.SignalProcessing)

exclude() (MACS3.IO.PeakIO.PeakIO method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) (MACS3.Signal.Region.Regions method) expand() (MACS3.Signal.Region.Regions method) extract_region_tags() (MACS3.Signal.FixWidthTrack.FWTrack method) extract_signals_from_regions() (in module MACS3.Signal.HMMR_Signal_Processing) extract_value() (MACS3.Signal.BedGraph.bedGraphTrackI method) extract_value_hmmr() (MACS3.Signal.BedGraph.bedGraphTrackI method)

F

factorial() (in module MACS3.Signal.Prob) fc (MACS3.IO.PeakIO.PeakContent attribute) fhd (MACS3.IO.Parser.GenericParser attribute) filename (MACS3.IO.BAM.BAIFile attribute) (MACS3.IO.Parser.GenericParser attribute) filter_dup() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) filter_fc() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.IO.PeakIO.PeakIO method) filter_pscore() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.IO.PeakIO.PeakIO method) filter_qscore() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.IO.PeakIO.PeakIO method) filter_score() (MACS3.IO.PeakIO.PeakIO method) (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method)

filterflag() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) finalize() (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) find_summit() (in module MACS3.Commands.refinepeak_cmd) fix_indels() (MACS3.Signal.PeakVariants.PeakVariants method) fraglengths() (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) fragMeans (MACS3.Signal.HMMR_EM.HMMR_EM attribute) FragParser (class in MACS3.IO.Parser) fragStddevs (MACS3.Signal.HMMR_EM.HMMR_EM attribute) fw (MACS3.Signal.FixWidthTrack.FWTrack attribute) FWTrack (class in MACS3.Signal.FixWidthTrack)

G

generate_digested_signals() (in module MACS3.Signal.HMMR_Signal_Processing) generate_states_path() (in module MACS3.Commands.hmmratac_cmd) generate_weight_mapping() (in module MACS3.Signal.HMMR_Signal_Processing) GenericParser (class in MACS3.IO.Parser) get_base_bq_by_ref_pos() (MACS3.Signal.ReadAlignment.ReadAlignment method) get_base_by_ref_pos() (MACS3.Signal.ReadAlignment.ReadAlignment method) get_bq_by_ref_pos() (MACS3.Signal.ReadAlignment.ReadAlignment method) get_chr_names() (MACS3.IO.PeakIO.PeakIO method) (MACS3.IO.PeakIO.RegionIO method) (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) (MACS3.Signal.Region.Regions method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) get_chromosomes() (MACS3.IO.BAM.BAMaccessor method) get_chunks_by_bin() (MACS3.IO.BAM.BAIFile method) get_chunks_by_list_of_bins() (MACS3.IO.BAM.BAIFile method) get_chunks_by_list_of_regions() (MACS3.IO.BAM.BAIFile method) get_chunks_by_region() (MACS3.IO.BAM.BAIFile method) get_coffset_by_region() (MACS3.IO.BAM.BAIFile method) get_coffsets_by_list_of_regions() (MACS3.IO.BAM.BAIFile method) get_data_by_chr() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method)

get_data_from_chrom() (MACS3.IO.PeakIO.PeakIO method) get_FASTQ() (MACS3.Signal.RACollection.RACollection method) (MACS3.Signal.ReadAlignment.ReadAlignment method) get_locations_by_chr() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) get_memory_usage() (MACS3.Utilities.Logger.MemoryLogger static method) get_metadata_by_refseq() (MACS3.IO.BAM.BAIFile method) get_PosReadsInfo_ref_pos() (MACS3.Signal.RACollection.RACollection method) (MACS3.Signal.UnitigRACollection.UnitigCollection method) get_reads_in_region() (MACS3.IO.BAM.BAMaccessor method) get_refer_biased_01s() (MACS3.Signal.PeakVariants.PeakVariants method) get_references() (MACS3.IO.Parser.BAMParser method) get_REFSEQ() (MACS3.Signal.ReadAlignment.ReadAlignment method) get_rlengths() (MACS3.IO.BAM.BAMaccessor method) (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) get_variant_bq_by_ref_pos() (MACS3.Signal.ReadAlignment.ReadAlignment method) (MACS3.Signal.UnitigRACollection.UnitigRAs method) guess_parser() (in module MACS3.IO.Parser) gzipped (MACS3.IO.Parser.GenericParser attribute)

H

has_indel() (MACS3.Signal.PeakVariants.PeakVariants method) has_refer_biased_01() (MACS3.Signal.PeakVariants.PeakVariants method) hmm_model_init() (in module MACS3.Signal.HMMR_HMM)

hmm_model_save() (in module MACS3.Signal.HMMR_HMM) hmm_predict() (in module MACS3.Signal.HMMR_HMM) hmm_training() (in module MACS3.Signal.HMMR_HMM) HMMR_EM (class in MACS3.Signal.HMMR_EM)

I

init_from_PeakIO() (MACS3.Signal.Region.Regions method) intersect() (MACS3.Signal.Region.Regions method) is_gzipped() (MACS3.IO.Parser.GenericParser method) is_indel() (MACS3.Signal.PeakVariants.Variant method)

is_only_del() (MACS3.Signal.PeakVariants.Variant method) is_only_insertion() (MACS3.Signal.PeakVariants.Variant method) is_refer_biased_01() (MACS3.Signal.PeakVariants.Variant method) is_sorted (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute)

L

lambda_bg (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) length (MACS3.IO.PeakIO.PeakContent attribute) (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) load_frag_files_options() (in module MACS3.Commands.callpeak_cmd) (in module MACS3.Commands.filterdup_cmd) (in module MACS3.Commands.pileup_cmd) (in module MACS3.Commands.predictd_cmd) (in module MACS3.Commands.randsample_cmd)

load_tag_files_options() (in module MACS3.Commands.callpeak_cmd) (in module MACS3.Commands.filterdup_cmd) (in module MACS3.Commands.pileup_cmd) (in module MACS3.Commands.predictd_cmd) (in module MACS3.Commands.randsample_cmd) (in module MACS3.Commands.refinepeak_cmd) locations (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute)

M

MACS3.Commands module MACS3.Commands.bdgbroadcall_cmd module MACS3.Commands.bdgcmp_cmd module MACS3.Commands.bdgdiff_cmd module MACS3.Commands.bdgopt_cmd module MACS3.Commands.bdgpeakcall_cmd module MACS3.Commands.callpeak_cmd module MACS3.Commands.callvar_cmd module MACS3.Commands.cmbreps_cmd module MACS3.Commands.filterdup_cmd module MACS3.Commands.hmmratac_cmd module MACS3.Commands.pileup_cmd module MACS3.Commands.predictd_cmd module MACS3.Commands.randsample_cmd module MACS3.Commands.refinepeak_cmd module MACS3.IO module MACS3.IO.BAM module MACS3.IO.BedGraphIO module MACS3.IO.OutputWriter module MACS3.IO.Parser module MACS3.IO.PeakIO module MACS3.Signal module MACS3.Signal.BedGraph module MACS3.Signal.CallPeakUnit module MACS3.Signal.FixWidthTrack module MACS3.Signal.HMMR_EM module MACS3.Signal.HMMR_HMM module MACS3.Signal.HMMR_Signal_Processing module MACS3.Signal.PairedEndTrack module MACS3.Signal.PeakDetect module MACS3.Signal.PeakModel module MACS3.Signal.PeakVariants module MACS3.Signal.Pileup module MACS3.Signal.PileupV2 module MACS3.Signal.PosReadsInfo module MACS3.Signal.Prob module MACS3.Signal.RACollection module MACS3.Signal.ReadAlignment module MACS3.Signal.Region module MACS3.Signal.ScoreTrack module

MACS3.Signal.SignalProcessing module MACS3.Signal.UnitigRACollection module MACS3.Signal.VariantStat module MACS3.Utilities module MACS3.Utilities.Constants module MACS3.Utilities.Logger module MACS3.Utilities.OptValidator module magic (MACS3.IO.BAM.BAIFile attribute) make_pq_table() (MACS3.Signal.ScoreTrack.ScoreTrackII method) make_ScoreTrackII_for_macs() (MACS3.Signal.BedGraph.bedGraphTrackI method) mapping_function_always_1() (in module MACS3.Signal.PileupV2) maxima() (in module MACS3.Signal.SignalProcessing) maxvalue (MACS3.Signal.BedGraph.bedGraphTrackI attribute) (MACS3.Signal.BedGraph.bedGraphTrackII attribute) MemoryLogger (class in MACS3.Utilities.Logger) merge_overlap() (MACS3.IO.PeakIO.RegionIO method) (MACS3.Signal.Region.Regions method) metadata (MACS3.IO.BAM.BAIFile attribute) min_tags (MACS3.Signal.PeakModel.PeakModel attribute) minus_line (MACS3.Signal.PeakModel.PeakModel attribute) minvalue (MACS3.Signal.BedGraph.bedGraphTrackI attribute) (MACS3.Signal.BedGraph.bedGraphTrackII attribute) model2r_script() (in module MACS3.IO.OutputWriter) module MACS3.Commands MACS3.Commands.bdgbroadcall_cmd MACS3.Commands.bdgcmp_cmd MACS3.Commands.bdgdiff_cmd MACS3.Commands.bdgopt_cmd MACS3.Commands.bdgpeakcall_cmd MACS3.Commands.callpeak_cmd MACS3.Commands.callvar_cmd MACS3.Commands.cmbreps_cmd MACS3.Commands.filterdup_cmd MACS3.Commands.hmmratac_cmd MACS3.Commands.pileup_cmd MACS3.Commands.predictd_cmd MACS3.Commands.randsample_cmd MACS3.Commands.refinepeak_cmd MACS3.IO MACS3.IO.BAM MACS3.IO.BedGraphIO MACS3.IO.OutputWriter MACS3.IO.Parser MACS3.IO.PeakIO MACS3.Signal MACS3.Signal.BedGraph MACS3.Signal.CallPeakUnit MACS3.Signal.FixWidthTrack MACS3.Signal.HMMR_EM MACS3.Signal.HMMR_HMM MACS3.Signal.HMMR_Signal_Processing MACS3.Signal.PairedEndTrack MACS3.Signal.PeakDetect MACS3.Signal.PeakModel MACS3.Signal.PeakVariants MACS3.Signal.Pileup MACS3.Signal.PileupV2 MACS3.Signal.PosReadsInfo MACS3.Signal.Prob MACS3.Signal.RACollection MACS3.Signal.ReadAlignment MACS3.Signal.Region MACS3.Signal.ScoreTrack MACS3.Signal.SignalProcessing MACS3.Signal.UnitigRACollection MACS3.Signal.VariantStat MACS3.Utilities MACS3.Utilities.Constants MACS3.Utilities.Logger MACS3.Utilities.OptValidator

N

n (MACS3.IO.Parser.BAMPEParser attribute) n_bins (MACS3.IO.BAM.BAIFile attribute) n_chunks (MACS3.IO.BAM.BAIFile attribute) n_edits_sum() (MACS3.Signal.RACollection.RACollection method) n_mapped (MACS3.IO.BAM.BAIFile attribute) n_ref (MACS3.IO.BAM.BAIFile attribute) n_unmapped (MACS3.IO.BAM.BAIFile attribute)

n_variants() (MACS3.Signal.PeakVariants.PeakVariants method) naive_call_peaks() (in module MACS3.Signal.Pileup) naive_quick_pileup() (in module MACS3.Signal.Pileup) name (MACS3.IO.PeakIO.PeakContent attribute) (MACS3.IO.PeakIO.PeakIO attribute), [1] no_lambda_flag (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) noffset_cache (MACS3.IO.BAM.BAMaccessor attribute) NotEnoughPairsException

O

opt_validate_bdgcmp() (in module MACS3.Utilities.OptValidator) opt_validate_bdgopt() (in module MACS3.Utilities.OptValidator) opt_validate_callpeak() (in module MACS3.Utilities.OptValidator) opt_validate_callvar() (in module MACS3.Utilities.OptValidator) opt_validate_cmbreps() (in module MACS3.Utilities.OptValidator) opt_validate_filterdup() (in module MACS3.Utilities.OptValidator)

opt_validate_hmmratac() (in module MACS3.Utilities.OptValidator) opt_validate_pileup() (in module MACS3.Utilities.OptValidator) opt_validate_predictd() (in module MACS3.Utilities.OptValidator) opt_validate_randsample() (in module MACS3.Utilities.OptValidator) opt_validate_refinepeak() (in module MACS3.Utilities.OptValidator) over_two_pv_array() (in module MACS3.Signal.Pileup) overlie() (MACS3.Signal.BedGraph.bedGraphTrackI method)

P

p2q() (MACS3.Signal.BedGraph.bedGraphTrackI method) pduplication() (in module MACS3.Signal.Prob) PE_mode (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) PeakContent (class in MACS3.IO.PeakIO) PeakDetect (class in MACS3.Signal.PeakDetect) PeakIO (class in MACS3.IO.PeakIO) PeakModel (class in MACS3.Signal.PeakModel) peaks (MACS3.IO.PeakIO.BroadPeakIO attribute), [1] (MACS3.IO.PeakIO.PeakIO attribute), [1] PeakVariants (class in MACS3.Signal.PeakVariants) PETrackI (class in MACS3.Signal.PairedEndTrack) PETrackII (class in MACS3.Signal.PairedEndTrack) pileup (MACS3.IO.PeakIO.PeakContent attribute) pileup_a_chromosome() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) pileup_a_chromosome_c() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) pileup_and_write_pe() (in module MACS3.Signal.Pileup) pileup_and_write_se() (in module MACS3.Signal.Pileup)

pileup_bdg() (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) pileup_bdg2() (MACS3.Signal.PairedEndTrack.PETrackII method) pileup_bdg_hmmr() (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) pileup_from_LR() (in module MACS3.Signal.PileupV2) pileup_from_LR_hmmratac() (in module MACS3.Signal.PileupV2) pileup_from_LRC() (in module MACS3.Signal.PileupV2) pileup_from_PN() (in module MACS3.Signal.PileupV2) plus_line (MACS3.Signal.PeakModel.PeakModel attribute) pnorm() (in module MACS3.Signal.Prob) pnorm2() (in module MACS3.Signal.Prob) poisson_cdf() (in module MACS3.Signal.Prob) poisson_cdf_inv() (in module MACS3.Signal.Prob) poisson_cdf_Q_inv() (in module MACS3.Signal.Prob) poisson_pdf() (in module MACS3.Signal.Prob) pop() (MACS3.Signal.Region.Regions method) PosReadsInfo (class in MACS3.Signal.PosReadsInfo) print_to_bed() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) pscore (MACS3.IO.PeakIO.PeakContent attribute) pseudocount (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)

Q

qscore (MACS3.IO.PeakIO.PeakContent attribute)

quick_pileup() (in module MACS3.Signal.Pileup)

R

RACollection (class in MACS3.Signal.RACollection) randomly_pick() (MACS3.IO.PeakIO.PeakIO method) raw_read_depth() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) read_bedGraph() (MACS3.IO.BedGraphIO.bedGraphIO method) read_from_xls() (MACS3.IO.PeakIO.PeakIO method) ReadAlignment (class in MACS3.Signal.ReadAlignment) references (MACS3.IO.BAM.BAMaccessor attribute) refine_peaks() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) RegionIO (class in MACS3.IO.PeakIO) Regions (class in MACS3.Signal.Region) regions (MACS3.IO.PeakIO.RegionIO attribute) (MACS3.Signal.Region.Regions attribute), [1] remove_outliers() (MACS3.Signal.RACollection.RACollection method) remove_variant() (MACS3.Signal.PeakVariants.PeakVariants method) replace_variant() (MACS3.Signal.PeakVariants.PeakVariants method) reset_baseline() (MACS3.Signal.BedGraph.bedGraphTrackI method)

rlengths (MACS3.IO.BAM.BAMaccessor attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) run() (in module MACS3.Commands.bdgbroadcall_cmd) (in module MACS3.Commands.bdgcmp_cmd) (in module MACS3.Commands.bdgdiff_cmd) (in module MACS3.Commands.bdgopt_cmd) (in module MACS3.Commands.bdgpeakcall_cmd) (in module MACS3.Commands.callpeak_cmd) (in module MACS3.Commands.callvar_cmd) (in module MACS3.Commands.cmbreps_cmd) (in module MACS3.Commands.filterdup_cmd) (in module MACS3.Commands.hmmratac_cmd) (in module MACS3.Commands.pileup_cmd) (in module MACS3.Commands.predictd_cmd) (in module MACS3.Commands.randsample_cmd) (in module MACS3.Commands.refinepeak_cmd)

S

SAMParser (class in MACS3.IO.Parser) sample_num() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) sample_num_copy() (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) sample_percent() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) sample_percent_copy() (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) save_accessible_regions() (in module MACS3.Commands.hmmratac_cmd) save_bedGraph (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) save_proba_to_bedGraph() (in module MACS3.Commands.hmmratac_cmd) save_SPMR (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) save_states_bed() (in module MACS3.Commands.hmmratac_cmd) savitzky_golay() (in module MACS3.Signal.SignalProcessing) savitzky_golay_order2_deriv1() (in module MACS3.Signal.SignalProcessing) scan_window (MACS3.Signal.PeakModel.PeakModel attribute) score (MACS3.IO.PeakIO.PeakContent attribute) ScoreTrackII (class in MACS3.Signal.ScoreTrack) se_all_in_one_pileup() (in module MACS3.Signal.Pileup) set_pseudocount() (MACS3.Signal.CallPeakUnit.CallerFromAlignments method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method)

set_rlengths() (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) set_single_value() (MACS3.Signal.BedGraph.bedGraphTrackI method) shifted_line (MACS3.Signal.PeakModel.PeakModel attribute) size (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) smooth() (in module MACS3.Signal.PeakModel) sniff() (MACS3.IO.Parser.BAMParser method) (MACS3.IO.Parser.GenericParser method) sort() (MACS3.IO.PeakIO.PeakIO method) (MACS3.IO.PeakIO.RegionIO method) (MACS3.Signal.FixWidthTrack.FWTrack method) (MACS3.Signal.PairedEndTrack.PETrackI method) (MACS3.Signal.PairedEndTrack.PETrackII method) (MACS3.Signal.RACollection.RACollection method) (MACS3.Signal.Region.Regions method) (MACS3.Signal.UnitigRACollection.UnitigCollection method) start (MACS3.IO.PeakIO.PeakContent attribute) subset() (MACS3.Signal.PairedEndTrack.PETrackII method) summary() (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) summit (MACS3.IO.PeakIO.PeakContent attribute)

T

tag_size (MACS3.IO.Parser.GenericParser attribute) to_summits_bed() (MACS3.IO.PeakIO.PeakIO method) to_vcf() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) tobed() (MACS3.IO.PeakIO.PeakIO method) top12alleles() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) top1isreference() (MACS3.Signal.PeakVariants.Variant method) top2isreference() (MACS3.Signal.PeakVariants.Variant method) total (MACS3.IO.PeakIO.PeakIO attribute), [1] (MACS3.Signal.FixWidthTrack.FWTrack attribute) (MACS3.Signal.PairedEndTrack.PETrackI attribute) (MACS3.Signal.PairedEndTrack.PETrackII attribute) (MACS3.Signal.Region.Regions attribute), [1]

total() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.Signal.BedGraph.bedGraphTrackI method) (MACS3.Signal.BedGraph.bedGraphTrackII method) total_length() (MACS3.Signal.Region.Regions method) toVariant() (MACS3.Signal.PosReadsInfo.PosReadsInfo method) toVCF() (MACS3.Signal.PeakVariants.PeakVariants method) (MACS3.Signal.PeakVariants.Variant method) trackline (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) treat (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) treat_scaling_factor (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute) tsize() (MACS3.IO.Parser.BAMParser method) (MACS3.IO.Parser.GenericParser method) TwoConditionScores (class in MACS3.Signal.ScoreTrack)

U

UnitigCollection (class in MACS3.Signal.UnitigRACollection)

UnitigRAs (class in MACS3.Signal.UnitigRACollection) update_top_alleles() (MACS3.Signal.PosReadsInfo.PosReadsInfo method)

V

Variant (class in MACS3.Signal.PeakVariants)

W

write_bedGraph() (MACS3.IO.BedGraphIO.bedGraphIO method) (MACS3.Signal.ScoreTrack.ScoreTrackII method) (MACS3.Signal.ScoreTrack.TwoConditionScores method) write_matrix() (MACS3.Signal.ScoreTrack.TwoConditionScores method) write_to_bed() (MACS3.IO.PeakIO.PeakIO method) (MACS3.IO.PeakIO.RegionIO method) (MACS3.Signal.Region.Regions method)

write_to_Bed12() (MACS3.IO.PeakIO.BroadPeakIO method) write_to_broadPeak() (MACS3.IO.PeakIO.BroadPeakIO method) write_to_gappedPeak() (MACS3.IO.PeakIO.BroadPeakIO method) write_to_narrowPeak() (MACS3.IO.PeakIO.PeakIO method) write_to_summit_bed() (MACS3.IO.PeakIO.PeakIO method) write_to_xls() (MACS3.IO.PeakIO.BroadPeakIO method) (MACS3.IO.PeakIO.PeakIO method)

X

xcorr (MACS3.Signal.PeakModel.PeakModel attribute)

Y

ycorr (MACS3.Signal.PeakModel.PeakModel attribute)

Z

zbdg_write() (in module MACS3.IO.OutputWriter)

zwig_write() (in module MACS3.IO.OutputWriter)