chromosight
stable
Tutorial
Example use of
chromosight
quantify
Plotting chromosight’s output
chromosight
chromosight
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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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H
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K
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L
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M
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N
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P
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R
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S
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V
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W
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X
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Z
B
bins_to_coords() (chromosight.utils.contacts_map.HicGenome method)
C
capture_ouput() (in module chromosight.cli.chromosight)
check_missing_mask() (in module chromosight.utils.preprocessing)
check_prefix_dir() (in module chromosight.utils.io)
chromosight (module)
chromosight.cli (module)
chromosight.cli.chromosight (module)
chromosight.kernels (module)
chromosight.utils (module)
chromosight.utils.contacts_map (module)
chromosight.utils.detection (module)
chromosight.utils.io (module)
chromosight.utils.plotting (module)
chromosight.utils.preprocessing (module)
chromosight.utils.stats (module)
chromosight.version (module)
click_finder() (in module chromosight.utils.plotting)
cmd_detect() (in module chromosight.cli.chromosight)
cmd_generate_config() (in module chromosight.cli.chromosight)
cmd_list_kernels() (in module chromosight.cli.chromosight)
cmd_quantify() (in module chromosight.cli.chromosight)
cmd_test() (in module chromosight.cli.chromosight)
compute_max_dist() (chromosight.utils.contacts_map.HicGenome method)
ContactMap (class in chromosight.utils.contacts_map)
coords_to_bins() (chromosight.utils.contacts_map.HicGenome method)
corr_to_pval() (in module chromosight.utils.stats)
create_mat() (chromosight.utils.contacts_map.ContactMap method)
crop_kernel() (in module chromosight.utils.preprocessing)
D
destroy_mat() (chromosight.utils.contacts_map.ContactMap method)
detrend() (chromosight.utils.contacts_map.ContactMap method)
(in module chromosight.utils.preprocessing)
diag_trim() (in module chromosight.utils.preprocessing)
distance_law() (in module chromosight.utils.preprocessing)
download_file() (in module chromosight.utils.io)
DumpMatrix (class in chromosight.utils.contacts_map)
E
erase_missing() (in module chromosight.utils.preprocessing)
F
factorise_kernel() (in module chromosight.utils.preprocessing)
fdr_correction() (in module chromosight.utils.stats)
filter_foci() (in module chromosight.utils.detection)
frame_missing_mask() (in module chromosight.utils.preprocessing)
G
gather_sub_matrices() (chromosight.utils.contacts_map.HicGenome method)
get_detectable_bins() (in module chromosight.utils.preprocessing)
get_full_mat_pattern() (chromosight.utils.contacts_map.HicGenome method)
get_sub_mat_pattern() (chromosight.utils.contacts_map.HicGenome method)
H
HicGenome (class in chromosight.utils.contacts_map)
K
keep_distance (chromosight.utils.contacts_map.ContactMap attribute)
L
label_foci() (in module chromosight.utils.detection)
load_bed2d() (in module chromosight.utils.io)
load_cool() (in module chromosight.utils.io)
load_kernel_config() (in module chromosight.utils.io)
logo_version() (in module chromosight.cli.chromosight)
M
main() (in module chromosight.cli.chromosight)
make_missing_mask() (in module chromosight.utils.preprocessing)
make_sub_matrices() (chromosight.utils.contacts_map.HicGenome method)
N
normalize() (chromosight.utils.contacts_map.HicGenome method)
normxcorr2() (in module chromosight.utils.detection)
P
pattern_detector() (in module chromosight.utils.detection)
pick_foci() (in module chromosight.utils.detection)
pileup_patterns() (in module chromosight.utils.detection)
pileup_plot() (in module chromosight.utils.plotting)
plot_whole_matrix() (in module chromosight.utils.plotting)
preprocess_inter_matrix() (chromosight.utils.contacts_map.ContactMap method)
preprocess_intra_matrix() (chromosight.utils.contacts_map.ContactMap method)
print_ascii_mat() (in module chromosight.utils.plotting)
progress() (in module chromosight.utils.io)
R
remove_diags() (chromosight.utils.contacts_map.ContactMap method)
remove_neighbours() (in module chromosight.utils.detection)
resize_kernel() (in module chromosight.utils.preprocessing)
S
save_windows() (in module chromosight.utils.io)
set_mat_diag() (in module chromosight.utils.preprocessing)
subsample() (chromosight.utils.contacts_map.ContactMap method)
subsample_contacts() (in module chromosight.utils.preprocessing)
sum_mat_bins() (in module chromosight.utils.preprocessing)
V
valid_to_missing() (in module chromosight.utils.preprocessing)
validate_patterns() (in module chromosight.utils.detection)
W
write_patterns() (in module chromosight.utils.io)
X
xcorr2() (in module chromosight.utils.detection)
Z
zero_pad_sparse() (in module chromosight.utils.preprocessing)
ztransform() (in module chromosight.utils.preprocessing)
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