coolpup.py
latest
Tutorials:
Guide to pileup analysis
Coolpuppy python API walkthrough notebook
Coolpuppy CLI walkthrough notebook
Distribution of TAD strength scores
API reference:
coolpup.py CLI
coolpuppy Python API
coolpup.py
Index
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Index
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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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G
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I
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L
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M
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N
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P
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S
_
__init__() (coolpuppy.coolpup.CoordCreator method)
(coolpuppy.coolpup.PileUpper method)
A
accumulate_stream() (coolpuppy.coolpup.PileUpper method)
accumulate_values() (in module coolpuppy.lib.puputils)
add_heatmap() (in module coolpuppy.plotpup)
add_score() (in module coolpuppy.plotpup)
add_stripe_lineplot() (in module coolpuppy.plotpup)
assign_groups() (in module coolpuppy.coolpup)
auto_rows_cols() (in module coolpuppy.plotpup)
B
bedpe2bed() (coolpuppy.coolpup.CoordCreator method)
bin_distance() (in module coolpuppy.lib.puputils)
bin_distance_intervals() (in module coolpuppy.coolpup)
C
coolpuppy.coolpup
module
coolpuppy.lib.io
module
coolpuppy.lib.numutils
module
coolpuppy.lib.puputils
module
coolpuppy.plotpup
module
CoordCreator (class in coolpuppy.coolpup)
corner_cv() (in module coolpuppy.lib.numutils)
D
divide_pups() (in module coolpuppy.lib.puputils)
E
empty_stream() (coolpuppy.coolpup.CoordCreator method)
expand() (in module coolpuppy.coolpup)
expand2D() (in module coolpuppy.coolpup)
F
filter_func_all() (coolpuppy.coolpup.CoordCreator method)
filter_func_chrom() (coolpuppy.coolpup.CoordCreator method)
filter_func_region() (coolpuppy.coolpup.CoordCreator method)
filter_func_trans_pairs() (coolpuppy.coolpup.CoordCreator method)
flip_mark_intervals_func() (in module coolpuppy.coolpup)
flip_snip_func() (in module coolpuppy.coolpup)
G
get_combinations() (coolpuppy.coolpup.CoordCreator method)
get_data() (coolpuppy.coolpup.PileUpper method)
get_domain_score() (in module coolpuppy.lib.numutils)
get_enrichment() (in module coolpuppy.lib.numutils)
get_expected_trans() (coolpuppy.coolpup.PileUpper method)
get_insulation_strength() (in module coolpuppy.lib.numutils)
get_intervals_stream() (coolpuppy.coolpup.CoordCreator method)
get_local_enrichment() (in module coolpuppy.lib.numutils)
get_min_max() (in module coolpuppy.plotpup)
get_score() (in module coolpuppy.lib.puputils)
group_by_region() (in module coolpuppy.lib.puputils)
I
is_gz_file() (in module coolpuppy.lib.io)
L
load_array_with_header() (in module coolpuppy.lib.io)
load_pileup_df() (in module coolpuppy.lib.io)
load_pileup_df_list() (in module coolpuppy.lib.io)
M
make_outmap() (coolpuppy.coolpup.PileUpper method)
module
coolpuppy.coolpup
coolpuppy.lib.io
coolpuppy.lib.numutils
coolpuppy.lib.puputils
coolpuppy.plotpup
N
norm_cis() (in module coolpuppy.lib.numutils)
norm_coverage() (in module coolpuppy.lib.puputils)
P
pileup() (in module coolpuppy.coolpup)
pileup_region() (coolpuppy.coolpup.PileUpper method)
PileUpper (class in coolpuppy.coolpup)
pileupsByDistanceWithControl() (coolpuppy.coolpup.PileUpper method)
pileupsByStrandByDistanceWithControl() (coolpuppy.coolpup.PileUpper method)
pileupsByStrandWithControl() (coolpuppy.coolpup.PileUpper method)
pileupsByWindowWithControl() (coolpuppy.coolpup.PileUpper method)
pileupsWithControl() (coolpuppy.coolpup.PileUpper method)
plot() (in module coolpuppy.plotpup)
plot_stripes() (in module coolpuppy.plotpup)
process() (coolpuppy.coolpup.CoordCreator method)
S
save_array_with_header() (in module coolpuppy.lib.io)
save_pileup_df() (in module coolpuppy.lib.io)
sniff_for_header() (in module coolpuppy.lib.io)
sort_separation() (in module coolpuppy.plotpup)
sum_pups() (in module coolpuppy.lib.puputils)
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