HiFive
latest
Introduction
Getting started
Restriction Fragment Handling
Loading Data
Filtering Data
Distance-Dependence Estimation
Normalizing Data
Binning Strategies
Multi-Resolution Heatmap
QuASAR Hi-C Scoring
Using HiFive
Tutorial for 5C Classes
Tutorial for HiC Classes
HiFive’s API
Release History
HiFive
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Index
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Index
A
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B
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C
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D
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E
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F
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H
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L
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P
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Q
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R
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S
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T
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W
A
add_hdf5_feature() (hifive.fend.Fend method)
B
bin_cis_array() (in module hifive.fivec_binning)
(in module hifive.hic_binning)
bin_trans_array() (in module hifive.hic_binning)
C
calculate_quality() (hifive.hic.HiC method)
calculate_replicate_quality() (hifive.hic.HiC method)
cis_heatmap() (hifive.fivec.FiveC method)
(hifive.hic.HiC method)
close() (hifive.quasar.Quasar method)
D
dynamically_bin_cis_array() (in module hifive.fivec_binning)
(in module hifive.hic_binning)
dynamically_bin_trans_array() (in module hifive.fivec_binning)
(in module hifive.hic_binning)
E
export_to_mat() (hifive.hic_data.HiCData method)
F
Fend (class in hifive.fend)
filter_fends() (hifive.hic.HiC method)
filter_fragments() (hifive.fivec.FiveC method)
find_binning_fend_corrections() (hifive.hic.HiC method)
find_binning_fragment_corrections() (hifive.fivec.FiveC method)
find_cis_signal() (in module hifive.fivec_binning)
(in module hifive.hic_binning)
find_cis_subregion_signal() (in module hifive.hic_binning)
find_distance_parameters() (hifive.fivec.FiveC method)
(hifive.hic.HiC method)
find_express_fend_corrections() (hifive.hic.HiC method)
find_express_fragment_corrections() (hifive.fivec.FiveC method)
find_multiresolution_heatmap() (in module hifive.hic_binning)
find_probability_fend_corrections() (hifive.hic.HiC method)
find_probability_fragment_corrections() (hifive.fivec.FiveC method)
find_quality_scores() (hifive.quasar.Quasar method)
find_replicate_scores() (hifive.quasar.Quasar method)
find_trans_mean() (hifive.fivec.FiveC method)
find_trans_means() (hifive.hic.HiC method)
find_trans_signal() (in module hifive.fivec_binning)
(in module hifive.hic_binning)
find_transformation() (hifive.quasar.Quasar method)
FiveC (class in hifive.fivec)
FiveCData (class in hifive.fivec_data)
Fragment (class in hifive.fragment)
H
HiC (class in hifive.hic)
HiCData (class in hifive.hic_data)
hifive.fend (module)
hifive.fivec (module)
hifive.fivec_binning (module)
hifive.fivec_data (module)
hifive.fragment (module)
hifive.hic (module)
hifive.hic_binning (module)
hifive.hic_data (module)
hifive.plotting (module)
hifive.quasar (module)
L
learn_fend_3D_model() (hifive.hic.HiC method)
load() (hifive.fend.Fend method)
(hifive.fivec.FiveC method)
(hifive.fivec_data.FiveCData method)
(hifive.fragment.Fragment method)
(hifive.hic.HiC method)
(hifive.hic_data.HiCData method)
(hifive.quasar.Quasar method)
load_binned_data_from_matrices() (hifive.hic_data.HiCData method)
load_bins() (hifive.fend.Fend method)
load_data() (hifive.fivec.FiveC method)
(hifive.hic.HiC method)
load_data_from_bam() (hifive.fivec_data.FiveCData method)
(hifive.hic_data.HiCData method)
load_data_from_counts() (hifive.fivec_data.FiveCData method)
load_data_from_mat() (hifive.hic_data.HiCData method)
load_data_from_raw() (hifive.hic_data.HiCData method)
load_fends() (hifive.fend.Fend method)
load_fragments() (hifive.fragment.Fragment method)
P
plot_compact_array() (in module hifive.plotting)
plot_diagonal_from_compact_array() (in module hifive.plotting)
plot_diagonal_from_upper_array() (in module hifive.plotting)
plot_fivec_compact_heatmap_dict() (in module hifive.plotting)
plot_fivec_dict() (in module hifive.plotting)
plot_fivec_heatmap() (in module hifive.plotting)
plot_full_array() (in module hifive.plotting)
plot_hic_heatmap() (in module hifive.plotting)
plot_key() (in module hifive.plotting)
plot_upper_array() (in module hifive.plotting)
print_report() (hifive.quasar.Quasar method)
Q
Quasar (class in hifive.quasar)
R
reset_filter() (hifive.hic.HiC method)
S
save() (hifive.fend.Fend method)
(hifive.fivec.FiveC method)
(hifive.fivec_data.FiveCData method)
(hifive.fragment.Fragment method)
(hifive.hic.HiC method)
(hifive.hic_data.HiCData method)
(hifive.quasar.Quasar method)
T
trans_heatmap() (hifive.fivec.FiveC method)
(hifive.hic.HiC method)
W
write_heatmap() (hifive.fivec.FiveC method)
(hifive.hic.HiC method)
write_heatmap_dict() (in module hifive.fivec_binning)
(in module hifive.hic_binning)
write_multiresolution_heatmap() (hifive.hic.HiC method)
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