MACS3
INSTALL Guide For MACS3
Subcommands
File Formats
Tutorial
Common Q & A
Contributor Covenant Code of Conduct
Contributing to MACS project
MACS3 API reference
MACS3
Index
Index
_
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A
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B
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C
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D
|
E
|
F
|
G
|
H
|
I
|
J
|
L
|
M
|
N
|
O
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P
|
Q
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R
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S
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T
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U
|
V
|
W
|
X
|
Y
_
__flag_sorted (MACS3.IO.PeakIO.RegionIO attribute)
A
add() (MACS3.IO.PeakIO.BroadPeakIO method)
(MACS3.IO.PeakIO.PeakIO method)
(MACS3.Signal.ScoreTrack.ScoreTrackII method)
(MACS3.Signal.ScoreTrack.TwoConditionScores 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)
(MACS3.Signal.ScoreTrack.TwoConditionScores 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_to_unitig_list() (MACS3.Signal.RACollection.RACollection method)
add_variant() (MACS3.Signal.PeakVariants.PeakVariants method)
align_unitig_to_REFSEQ() (MACS3.Signal.RACollection.RACollection method)
aln_length (MACS3.Signal.UnitigRACollection.UnitigRAs attribute)
alt_allele (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
alternative_d (MACS3.Signal.PeakModel.PeakModel attribute)
annotation (MACS3.Signal.FixWidthTrack.FWTrack attribute)
(MACS3.Signal.PairedEndTrack.PETrackI attribute)
(MACS3.Signal.PairedEndTrack.PETrackII attribute)
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
barcode_dict (MACS3.Signal.PairedEndTrack.PETrackII attribute)
barcode_last_n (MACS3.Signal.PairedEndTrack.PETrackII attribute)
barcodes (MACS3.Signal.PairedEndTrack.PETrackII attribute)
baseline_value (MACS3.Signal.BedGraph.bedGraphTrackI attribute)
(MACS3.Signal.BedGraph.bedGraphTrackII attribute)
bedGraph_control_filename (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
bedGraph_ctrl_f (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
bedGraph_filename_prefix (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
bedGraph_treat_f (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
bedGraph_treat_filename (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
bedGraphTrackI (class in MACS3.Signal.BedGraph)
bedGraphTrackII (class in MACS3.Signal.BedGraph)
BIC_heter_AS (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
BIC_heter_noAS (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
BIC_homo_major (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
BIC_homo_minor (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
binaryqual (MACS3.Signal.ReadAlignment.ReadAlignment attribute)
binaryseq (MACS3.Signal.ReadAlignment.ReadAlignment attribute)
binomial_cdf() (in module MACS3.Signal.Prob)
binomial_cdf_inv() (in module MACS3.Signal.Prob)
binomial_coef() (in module MACS3.Signal.Prob)
binomial_pdf() (in module MACS3.Signal.Prob)
binomial_sf() (in module MACS3.Signal.Prob)
blockNum (MACS3.IO.PeakIO.BroadPeakContent attribute)
blockSizes (MACS3.IO.PeakIO.BroadPeakContent attribute)
blockStarts (MACS3.IO.PeakIO.BroadPeakContent attribute)
bool() (in module MACS3.Signal.BedGraph)
(in module MACS3.Signal.FixWidthTrack)
(in module MACS3.Signal.PairedEndTrack)
(in module MACS3.Signal.PeakModel)
(in module MACS3.Signal.PeakVariants)
(in module MACS3.Signal.PosReadsInfo)
(in module MACS3.Signal.Prob)
(in module MACS3.Signal.RACollection)
(in module MACS3.Signal.ReadAlignment)
(in module MACS3.Signal.Region)
(in module MACS3.Signal.ScoreTrack)
(in module MACS3.Signal.SignalProcessing)
(in module MACS3.Signal.UnitigRACollection)
(in module MACS3.Signal.VariantStat)
bq_set_C (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
bq_set_T (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
BroadPeakContent (class in MACS3.IO.PeakIO)
BroadPeakIO (class in MACS3.IO.PeakIO)
buf_size (MACS3.Signal.FixWidthTrack.FWTrack attribute)
(MACS3.Signal.PairedEndTrack.PETrackI attribute)
(MACS3.Signal.PairedEndTrack.PETrackII attribute)
buffer_size (MACS3.Signal.BedGraph.bedGraphTrackII 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_chromosome() (MACS3.Signal.ScoreTrack.TwoConditionScores method)
build_unitig_collection() (MACS3.Signal.RACollection.RACollection method)
bw (MACS3.Signal.PeakModel.PeakModel attribute)
C
c1bdg (MACS3.Signal.ScoreTrack.TwoConditionScores attribute)
c2bdg (MACS3.Signal.ScoreTrack.TwoConditionScores attribute)
calculate_elbows() (in module MACS3.Signal.BedGraph)
calculate_GQ() (in module MACS3.Signal.VariantStat)
calculate_GQ_heterASsig() (in module MACS3.Signal.VariantStat)
calculate_ln() (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)
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)
chisq_logp_e() (in module MACS3.Signal.Prob)
chisq_pvalue_e() (in module MACS3.Signal.Prob)
chr_pos_treat_ctrl (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
chrom (MACS3.IO.PeakIO.PeakContent attribute)
,
[1]
(MACS3.Signal.PeakVariants.PeakVariants attribute)
(MACS3.Signal.RACollection.RACollection attribute)
(MACS3.Signal.ReadAlignment.ReadAlignment attribute)
(MACS3.Signal.UnitigRACollection.UnitigCollection attribute)
(MACS3.Signal.UnitigRACollection.UnitigRAs attribute)
chromosomes (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
cigar (MACS3.Signal.ReadAlignment.ReadAlignment attribute)
clean_up_ndarray() (in module MACS3.Signal.CallPeakUnit)
(in module MACS3.Signal.Pileup)
(in module MACS3.Signal.PileupV2)
CO_sorted (MACS3.IO.PeakIO.PeakIO attribute)
,
[1]
compute_foldenrichment() (MACS3.Signal.ScoreTrack.ScoreTrackII method)
compute_likelihood() (MACS3.Signal.ScoreTrack.ScoreTrackII method)
compute_logFE() (MACS3.Signal.ScoreTrack.ScoreTrackII method)
compute_max() (MACS3.Signal.ScoreTrack.ScoreTrackII method)
compute_pvalue() (MACS3.Signal.ScoreTrack.ScoreTrackII method)
compute_qvalue() (MACS3.Signal.ScoreTrack.ScoreTrackII method)
compute_region_tags_from_peaks() (MACS3.Signal.FixWidthTrack.FWTrack method)
compute_SPMR() (MACS3.Signal.ScoreTrack.ScoreTrackII method)
compute_subtraction() (MACS3.Signal.ScoreTrack.ScoreTrackII method)
compute_sym_likelihood() (MACS3.Signal.ScoreTrack.ScoreTrackII method)
cond1_factor (MACS3.Signal.ScoreTrack.TwoConditionScores attribute)
cond2_factor (MACS3.Signal.ScoreTrack.TwoConditionScores attribute)
converged (MACS3.Signal.HMMR_EM.HMMR_EM attribute)
count_fraglengths() (MACS3.Signal.PairedEndTrack.PETrackI method)
(MACS3.Signal.PairedEndTrack.PETrackII method)
ctrl (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
ctrl_d_s (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
ctrl_edm (MACS3.Signal.ScoreTrack.ScoreTrackII attribute)
ctrl_scaling_factor_s (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
cutoff (MACS3.Signal.ScoreTrack.ScoreTrackII attribute)
(MACS3.Signal.ScoreTrack.TwoConditionScores attribute)
cutoff_analysis() (MACS3.Signal.BedGraph.bedGraphTrackI method)
(MACS3.Signal.ScoreTrack.ScoreTrackII method)
cutoff_analysis_filename (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
D
d (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
(MACS3.Signal.PeakModel.PeakModel attribute)
d_min (MACS3.Signal.PeakModel.PeakModel attribute)
d_Variants (MACS3.Signal.PeakVariants.PeakVariants attribute)
data (MACS3.Signal.ScoreTrack.ScoreTrackII attribute)
(MACS3.Signal.ScoreTrack.TwoConditionScores attribute)
datalength (MACS3.Signal.ScoreTrack.ScoreTrackII attribute)
(MACS3.Signal.ScoreTrack.TwoConditionScores attribute)
debug (MACS3.Signal.PeakModel.PeakModel attribute)
deltaBIC (MACS3.Signal.PosReadsInfo.PosReadsInfo 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)
divide_func() (in module MACS3.Signal.BedGraph)
E
enable_trackline() (MACS3.Signal.CallPeakUnit.CallerFromAlignments method)
(MACS3.Signal.ScoreTrack.ScoreTrackII method)
end (MACS3.IO.PeakIO.BroadPeakContent attribute)
(MACS3.IO.PeakIO.PeakContent attribute)
,
[1]
(MACS3.Signal.PeakVariants.PeakVariants attribute)
end_shift (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
enforce_peakyness() (in module MACS3.Signal.SignalProcessing)
enforce_valleys() (in module MACS3.Signal.SignalProcessing)
epsilon (MACS3.Signal.HMMR_EM.HMMR_EM attribute)
error (MACS3.Signal.PeakModel.PeakModel attribute)
ex20() (in module MACS3.Signal.Prob)
exclude() (MACS3.IO.PeakIO.PeakIO method)
(MACS3.Signal.PairedEndTrack.PETrackI method)
(MACS3.Signal.PairedEndTrack.PETrackII method)
(MACS3.Signal.Region.Regions method)
exp() (in module MACS3.Signal.Prob)
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.BroadPeakContent attribute)
(MACS3.IO.PeakIO.PeakContent attribute)
,
[1]
fclose() (in module MACS3.Signal.CallPeakUnit)
fermi_assemble() (MACS3.Signal.RACollection.RACollection method)
fermiNTs (MACS3.Signal.PosReadsInfo.PosReadsInfo 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)
filter_unitig_with_bad_aln() (MACS3.Signal.RACollection.RACollection method)
filterflag() (MACS3.Signal.PosReadsInfo.PosReadsInfo method)
filterout (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
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_optimal_cutoff() (in module MACS3.Signal.CallPeakUnit)
fisher_func() (in module MACS3.Signal.BedGraph)
fix_coordinates() (in module MACS3.Signal.Pileup)
fix_indels() (MACS3.Signal.PeakVariants.PeakVariants method)
float32_t() (in module MACS3.Signal.Prob)
float64_t() (in module MACS3.Signal.Prob)
fraglengths() (MACS3.Signal.PairedEndTrack.PETrackI method)
(MACS3.Signal.PairedEndTrack.PETrackII method)
fragMeans (MACS3.Signal.HMMR_EM.HMMR_EM attribute)
fragStddevs (MACS3.Signal.HMMR_EM.HMMR_EM attribute)
fragVars (MACS3.Signal.HMMR_EM.HMMR_EM attribute)
free() (in module MACS3.Signal.Pileup)
(in module MACS3.Signal.RACollection)
fw (MACS3.Signal.FixWidthTrack.FWTrack attribute)
FWTrack (class in MACS3.Signal.FixWidthTrack)
G
generate_digested_signals() (in module MACS3.Signal.HMMR_Signal_Processing)
generate_weight_mapping() (in module MACS3.Signal.HMMR_Signal_Processing)
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_common_chrs() (MACS3.Signal.ScoreTrack.TwoConditionScores 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_from_multiple_scores() (in module MACS3.Signal.CallPeakUnit)
get_locations_by_chr() (MACS3.Signal.FixWidthTrack.FWTrack method)
(MACS3.Signal.PairedEndTrack.PETrackI method)
(MACS3.Signal.PairedEndTrack.PETrackII method)
get_logFE() (in module MACS3.Signal.ScoreTrack)
get_memory_usage() (MACS3.Utilities.Logger.MemoryLogger static method)
get_n_edits() (MACS3.Signal.ReadAlignment.ReadAlignment method)
get_PosReadsInfo_ref_pos() (MACS3.Signal.RACollection.RACollection method)
(MACS3.Signal.UnitigRACollection.UnitigCollection method)
get_pscore() (in module MACS3.Signal.ScoreTrack)
get_refer_biased_01s() (MACS3.Signal.PeakVariants.PeakVariants method)
get_REFSEQ() (MACS3.Signal.ReadAlignment.ReadAlignment method)
get_rlengths() (MACS3.Signal.FixWidthTrack.FWTrack method)
(MACS3.Signal.PairedEndTrack.PETrackI method)
(MACS3.Signal.PairedEndTrack.PETrackII method)
get_subtraction() (in module MACS3.Signal.ScoreTrack)
get_variant_bq_by_ref_pos() (MACS3.Signal.ReadAlignment.ReadAlignment method)
(MACS3.Signal.UnitigRACollection.UnitigRAs method)
get_weighted_density() (in module MACS3.Signal.HMMR_EM)
(in module MACS3.Signal.HMMR_HMM)
(in module MACS3.Signal.HMMR_Signal_Processing)
getitem_then_subtract() (in module MACS3.Signal.CallPeakUnit)
GQ (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
GQ_heter_AS (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
GQ_heter_ASsig (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
GQ_heter_noAS (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
GQ_homo_major (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
GreedyMaxFunctionAS() (in module MACS3.Signal.VariantStat)
GreedyMaxFunctionNoAS() (in module MACS3.Signal.VariantStat)
GT (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
gz (MACS3.Signal.PeakModel.PeakModel attribute)
H
hard_clip() (in module MACS3.Signal.SignalProcessing)
has_indel() (MACS3.Signal.PeakVariants.PeakVariants method)
has_refer_biased_01() (MACS3.Signal.PeakVariants.PeakVariants method)
hasfermiinfor (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
heter_AS_alleleratio (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
heter_AS_kc (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
heter_AS_ki (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
heter_noAS_kc (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
heter_noAS_ki (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
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
info (MACS3.Signal.PeakModel.PeakModel attribute)
init_from_PeakIO() (MACS3.Signal.Region.Regions method)
int32_t() (in module MACS3.Signal.Prob)
int64_t() (in module MACS3.Signal.Prob)
int_max() (in module MACS3.Signal.ScoreTrack)
int_min() (in module MACS3.Signal.ScoreTrack)
internal_minima() (in module MACS3.Signal.SignalProcessing)
intersect() (MACS3.Signal.Region.Regions method)
is_destroyed (MACS3.Signal.FixWidthTrack.FWTrack attribute)
(MACS3.Signal.PairedEndTrack.PETrackI attribute)
(MACS3.Signal.PairedEndTrack.PETrackII attribute)
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.FixWidthTrack.FWTrack attribute)
(MACS3.Signal.PairedEndTrack.PETrackI attribute)
(MACS3.Signal.PairedEndTrack.PETrackII attribute)
(MACS3.Signal.UnitigRACollection.UnitigCollection attribute)
is_valid_peak() (in module MACS3.Signal.SignalProcessing)
J
jump (MACS3.Signal.HMMR_EM.HMMR_EM attribute)
L
l (MACS3.Signal.ReadAlignment.ReadAlignment attribute)
lambda_bg (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
left (MACS3.Signal.RACollection.RACollection attribute)
(MACS3.Signal.UnitigRACollection.UnitigCollection attribute)
left_forward() (in module MACS3.Signal.FixWidthTrack)
left_sum() (in module MACS3.Signal.FixWidthTrack)
length (MACS3.IO.PeakIO.BroadPeakContent attribute)
(MACS3.IO.PeakIO.PeakContent attribute)
,
[1]
(MACS3.Signal.FixWidthTrack.FWTrack attribute)
(MACS3.Signal.PairedEndTrack.PETrackI attribute)
(MACS3.Signal.PairedEndTrack.PETrackII attribute)
(MACS3.Signal.RACollection.RACollection attribute)
(MACS3.Signal.UnitigRACollection.UnitigCollection attribute)
lmfold (MACS3.Signal.PeakModel.PeakModel attribute)
lnL_heter_AS (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
lnL_heter_noAS (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
lnL_homo_major (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
lnL_homo_minor (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
locations (MACS3.Signal.FixWidthTrack.FWTrack attribute)
(MACS3.Signal.PairedEndTrack.PETrackI attribute)
(MACS3.Signal.PairedEndTrack.PETrackII attribute)
log() (in module MACS3.Signal.Prob)
(in module MACS3.Signal.ScoreTrack)
log10() (in module MACS3.Signal.BedGraph)
(in module MACS3.Signal.ScoreTrack)
log10_poisson_cdf_P_large_lambda() (in module MACS3.Signal.Prob)
log10_poisson_cdf_Q_large_lambda() (in module MACS3.Signal.Prob)
logLR_asym() (in module MACS3.Signal.ScoreTrack)
logLR_sym() (in module MACS3.Signal.ScoreTrack)
logspace_add() (in module MACS3.Signal.Prob)
lpos (MACS3.Signal.ReadAlignment.ReadAlignment attribute)
(MACS3.Signal.UnitigRACollection.UnitigRAs attribute)
M
MACS3.Commands
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
make_pq_table() (MACS3.Signal.ScoreTrack.ScoreTrackII method)
make_PV_from_LR() (in module MACS3.Signal.PileupV2)
make_PV_from_LRC() (in module MACS3.Signal.PileupV2)
make_PV_from_PN() (in module MACS3.Signal.PileupV2)
make_ScoreTrackII_for_macs() (MACS3.Signal.BedGraph.bedGraphTrackI method)
malloc() (in module MACS3.Signal.RACollection)
mapping_function_always_1() (in module MACS3.Signal.PileupV2)
max_fraglen (MACS3.Signal.HMMR_EM.HMMR_EM attribute)
max_pairnum (MACS3.Signal.PeakModel.PeakModel attribute)
max_tags (MACS3.Signal.PeakModel.PeakModel attribute)
maxima() (in module MACS3.Signal.SignalProcessing)
maxIter (MACS3.Signal.HMMR_EM.HMMR_EM attribute)
maxvalue (MACS3.Signal.BedGraph.bedGraphTrackI attribute)
(MACS3.Signal.BedGraph.bedGraphTrackII attribute)
MD (MACS3.Signal.ReadAlignment.ReadAlignment attribute)
mean() (in module MACS3.Signal.Pileup)
mean_from_peakcontent() (MACS3.Signal.ScoreTrack.TwoConditionScores method)
mean_func() (in module MACS3.Signal.BedGraph)
MemoryLogger (class in MACS3.Utilities.Logger)
merge_overlap() (MACS3.IO.PeakIO.RegionIO method)
(MACS3.Signal.Region.Regions method)
merge_regions() (MACS3.Signal.BedGraph.bedGraphTrackI method)
min_fraglen (MACS3.Signal.HMMR_EM.HMMR_EM 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)
module
MACS3.Commands
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
mutation_type (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
N
n_edits (MACS3.Signal.ReadAlignment.ReadAlignment attribute)
n_edits_sum() (MACS3.Signal.RACollection.RACollection method)
n_reads (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
n_reads_C (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
n_reads_T (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
n_strand (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
n_tips (MACS3.Signal.PosReadsInfo.PosReadsInfo 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.BroadPeakContent attribute)
(MACS3.IO.PeakIO.PeakContent attribute)
,
[1]
(MACS3.IO.PeakIO.PeakIO attribute)
,
[1]
no_lambda_flag (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
normalization_method (MACS3.Signal.ScoreTrack.ScoreTrackII attribute)
normalize() (MACS3.Signal.ScoreTrack.ScoreTrackII method)
NotEnoughPairsException
O
online_update() (in module MACS3.Signal.HMMR_EM)
optimal_p_cutoff (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
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)
,
[1]
peak (MACS3.Signal.RACollection.RACollection attribute)
(MACS3.Signal.UnitigRACollection.UnitigCollection attribute)
peak_refseq (MACS3.Signal.RACollection.RACollection attribute)
peak_refseq_ext (MACS3.Signal.RACollection.RACollection 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]
peaksize (MACS3.Signal.PeakModel.PeakModel attribute)
PeakVariants (class in MACS3.Signal.PeakVariants)
PETrackI (class in MACS3.Signal.PairedEndTrack)
PETrackII (class in MACS3.Signal.PairedEndTrack)
pileup (MACS3.IO.PeakIO.BroadPeakContent attribute)
(MACS3.IO.PeakIO.PeakContent attribute)
,
[1]
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_data_files (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
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)
pileup_PV() (in module MACS3.Signal.PileupV2)
pileup_treat_ctrl_a_chromosome() (MACS3.Signal.CallPeakUnit.CallerFromAlignments method)
PL_00 (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
PL_01 (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
PL_11 (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
plus_line (MACS3.Signal.PeakModel.PeakModel attribute)
pnorm() (in module MACS3.Signal.Prob)
pnorm2() (in module MACS3.Signal.Prob)
pointer (MACS3.Signal.FixWidthTrack.FWTrack attribute)
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)
poz() (in module MACS3.Signal.Prob)
pqtable (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
print_to_bed() (MACS3.Signal.FixWidthTrack.FWTrack method)
(MACS3.Signal.PairedEndTrack.PETrackI method)
product_func() (in module MACS3.Signal.BedGraph)
pscore (MACS3.IO.PeakIO.BroadPeakContent attribute)
(MACS3.IO.PeakIO.PeakContent attribute)
,
[1]
pseudocount (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
(MACS3.Signal.ScoreTrack.ScoreTrackII attribute)
(MACS3.Signal.ScoreTrack.TwoConditionScores attribute)
pvalue_all_done (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
pvalue_length (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
pvalue_npeaks (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
pvalue_stat (MACS3.Signal.ScoreTrack.ScoreTrackII attribute)
pvalue_stat1 (MACS3.Signal.ScoreTrack.TwoConditionScores attribute)
pvalue_stat2 (MACS3.Signal.ScoreTrack.TwoConditionScores attribute)
pvalue_stat3 (MACS3.Signal.ScoreTrack.TwoConditionScores attribute)
Q
qscore (MACS3.IO.PeakIO.BroadPeakContent attribute)
(MACS3.IO.PeakIO.PeakContent attribute)
,
[1]
QUAL (MACS3.Signal.ReadAlignment.ReadAlignment attribute)
quick_pileup() (in module MACS3.Signal.Pileup)
R
RACollection (class in MACS3.Signal.RACollection)
RAlists (MACS3.Signal.RACollection.RACollection attribute)
(MACS3.Signal.UnitigRACollection.UnitigRAs attribute)
randomly_pick() (MACS3.IO.PeakIO.PeakIO method)
RAs_left (MACS3.Signal.RACollection.RACollection attribute)
RAs_right (MACS3.Signal.RACollection.RACollection attribute)
raw_read_depth() (MACS3.Signal.PosReadsInfo.PosReadsInfo method)
read_from_xls() (MACS3.IO.PeakIO.PeakIO method)
ReadAlignment (class in MACS3.Signal.ReadAlignment)
readname (MACS3.Signal.ReadAlignment.ReadAlignment attribute)
ref_allele (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
ref_pos (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
reference_aln (MACS3.Signal.UnitigRACollection.UnitigRAs attribute)
reference_length (MACS3.Signal.UnitigRACollection.UnitigRAs attribute)
refine_peaks() (MACS3.Signal.BedGraph.bedGraphTrackI method)
(MACS3.Signal.BedGraph.bedGraphTrackII method)
refseq (MACS3.Signal.PeakVariants.PeakVariants attribute)
RegionIO (class in MACS3.IO.PeakIO)
Regions (class in MACS3.Signal.Region)
regions (MACS3.IO.PeakIO.RegionIO attribute)
,
[1]
(MACS3.Signal.Region.Regions attribute)
,
[1]
relative_ref_pos_to_relative_query_pos() (MACS3.Signal.ReadAlignment.ReadAlignment method)
remap_RAs_w_unitigs() (MACS3.Signal.RACollection.RACollection method)
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)
return_greater() (in module MACS3.Signal.HMMR_EM)
right (MACS3.Signal.RACollection.RACollection attribute)
(MACS3.Signal.UnitigRACollection.UnitigCollection attribute)
right_forward() (in module MACS3.Signal.FixWidthTrack)
right_sum() (in module MACS3.Signal.FixWidthTrack)
rlengths (MACS3.Signal.FixWidthTrack.FWTrack attribute)
(MACS3.Signal.PairedEndTrack.PETrackI attribute)
(MACS3.Signal.PairedEndTrack.PETrackII attribute)
rpos (MACS3.Signal.ReadAlignment.ReadAlignment attribute)
(MACS3.Signal.UnitigRACollection.UnitigRAs attribute)
S
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)
sample_percentage (MACS3.Signal.HMMR_EM.HMMR_EM attribute)
save_bedGraph (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
save_SPMR (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
savitzky_golay() (in module MACS3.Signal.SignalProcessing)
savitzky_golay_order2_deriv1() (in module MACS3.Signal.SignalProcessing)
SB_score_ATAC() (MACS3.Signal.PosReadsInfo.PosReadsInfo method)
SB_score_ChIP() (MACS3.Signal.PosReadsInfo.PosReadsInfo method)
scan_window (MACS3.Signal.PeakModel.PeakModel attribute)
score (MACS3.IO.PeakIO.BroadPeakContent attribute)
(MACS3.IO.PeakIO.PeakContent attribute)
,
[1]
ScoreTrackII (class in MACS3.Signal.ScoreTrack)
scoring_method (MACS3.Signal.ScoreTrack.ScoreTrackII attribute)
se_all_in_one_pileup() (in module MACS3.Signal.Pileup)
seed (MACS3.Signal.HMMR_EM.HMMR_EM attribute)
SEQ (MACS3.Signal.ReadAlignment.ReadAlignment attribute)
seq (MACS3.Signal.UnitigRACollection.UnitigRAs attribute)
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)
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)
sorted (MACS3.Signal.RACollection.RACollection attribute)
sqrt() (in module MACS3.Signal.BedGraph)
(in module MACS3.Signal.SignalProcessing)
start (MACS3.IO.PeakIO.BroadPeakContent attribute)
(MACS3.IO.PeakIO.PeakContent attribute)
,
[1]
(MACS3.Signal.PeakVariants.PeakVariants attribute)
strand (MACS3.Signal.ReadAlignment.ReadAlignment attribute)
subpeak_letters() (in module MACS3.IO.PeakIO)
(in module MACS3.Signal.PeakDetect)
subset() (MACS3.Signal.PairedEndTrack.PETrackII method)
subtract_func() (in module MACS3.Signal.BedGraph)
summary (MACS3.Signal.PeakModel.PeakModel attribute)
summary() (MACS3.Signal.BedGraph.bedGraphTrackI method)
(MACS3.Signal.BedGraph.bedGraphTrackII method)
summit (MACS3.IO.PeakIO.PeakContent attribute)
,
[1]
T
t1bdg (MACS3.Signal.ScoreTrack.TwoConditionScores attribute)
t2bdg (MACS3.Signal.ScoreTrack.TwoConditionScores attribute)
tag_expansion_size (MACS3.Signal.PeakModel.PeakModel attribute)
thickEnd (MACS3.IO.PeakIO.BroadPeakContent attribute)
thickStart (MACS3.IO.PeakIO.BroadPeakContent attribute)
to_summits_bed() (MACS3.IO.PeakIO.PeakIO method)
to_vcf() (MACS3.Signal.PosReadsInfo.PosReadsInfo method)
tobed() (MACS3.IO.PeakIO.PeakIO method)
too_flat() (in module MACS3.Signal.SignalProcessing)
top12alleles() (MACS3.Signal.PosReadsInfo.PosReadsInfo method)
top12alleles_ratio (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
top1allele (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
top1isreference() (MACS3.Signal.PeakVariants.Variant method)
top2allele (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
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)
(MACS3.Signal.ScoreTrack.ScoreTrackII method)
(MACS3.Signal.ScoreTrack.TwoConditionScores 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)
,
[1]
(MACS3.Signal.ScoreTrack.ScoreTrackII attribute)
treat (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
treat_edm (MACS3.Signal.ScoreTrack.ScoreTrackII attribute)
treat_scaling_factor (MACS3.Signal.CallPeakUnit.CallerFromAlignments attribute)
,
[1]
treatment (MACS3.Signal.PeakModel.PeakModel attribute)
TwoConditionScores (class in MACS3.Signal.ScoreTrack)
type (MACS3.Signal.PosReadsInfo.PosReadsInfo attribute)
U
uint32_t() (in module MACS3.Signal.Prob)
uint64_t() (in module MACS3.Signal.Prob)
umfold (MACS3.Signal.PeakModel.PeakModel attribute)
unitig_aln (MACS3.Signal.UnitigRACollection.UnitigRAs attribute)
unitig_length (MACS3.Signal.UnitigRACollection.UnitigRAs attribute)
UnitigCollection (class in MACS3.Signal.UnitigRACollection)
UnitigRAs (class in MACS3.Signal.UnitigRACollection)
update_top_alleles() (MACS3.Signal.PosReadsInfo.PosReadsInfo method)
URAs_left (MACS3.Signal.UnitigRACollection.UnitigCollection attribute)
URAs_list (MACS3.Signal.UnitigRACollection.UnitigCollection attribute)
URAs_right (MACS3.Signal.UnitigRACollection.UnitigCollection attribute)
V
v_alt_allele (MACS3.Signal.PeakVariants.Variant attribute)
v_AR (MACS3.Signal.PeakVariants.Variant attribute)
v_BIC_heter_AS (MACS3.Signal.PeakVariants.Variant attribute)
v_BIC_heter_noAS (MACS3.Signal.PeakVariants.Variant attribute)
v_BIC_homo_major (MACS3.Signal.PeakVariants.Variant attribute)
v_BIC_homo_minor (MACS3.Signal.PeakVariants.Variant attribute)
v_deltaBIC (MACS3.Signal.PeakVariants.Variant attribute)
v_DP (MACS3.Signal.PeakVariants.Variant attribute)
v_DP1C (MACS3.Signal.PeakVariants.Variant attribute)
v_DP1T (MACS3.Signal.PeakVariants.Variant attribute)
v_DP2C (MACS3.Signal.PeakVariants.Variant attribute)
v_DP2T (MACS3.Signal.PeakVariants.Variant attribute)
v_DPC (MACS3.Signal.PeakVariants.Variant attribute)
v_DPT (MACS3.Signal.PeakVariants.Variant attribute)
v_filter (MACS3.Signal.PeakVariants.Variant attribute)
v_GQ (MACS3.Signal.PeakVariants.Variant attribute)
v_GT (MACS3.Signal.PeakVariants.Variant attribute)
v_MINUS1T (MACS3.Signal.PeakVariants.Variant attribute)
v_MINUS2T (MACS3.Signal.PeakVariants.Variant attribute)
v_mutation_type (MACS3.Signal.PeakVariants.Variant attribute)
v_PL_00 (MACS3.Signal.PeakVariants.Variant attribute)
v_PL_01 (MACS3.Signal.PeakVariants.Variant attribute)
v_PL_11 (MACS3.Signal.PeakVariants.Variant attribute)
v_PLUS1T (MACS3.Signal.PeakVariants.Variant attribute)
v_PLUS2T (MACS3.Signal.PeakVariants.Variant attribute)
v_ref_allele (MACS3.Signal.PeakVariants.Variant attribute)
v_ref_pos (MACS3.Signal.PeakVariants.Variant attribute)
v_top1allele (MACS3.Signal.PeakVariants.Variant attribute)
v_top2allele (MACS3.Signal.PeakVariants.Variant attribute)
v_type (MACS3.Signal.PeakVariants.Variant attribute)
Variant (class in MACS3.Signal.PeakVariants)
verify_alns() (MACS3.Signal.RACollection.RACollection method)
W
warn (MACS3.Signal.PeakModel.PeakModel attribute)
write_bedGraph() (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)