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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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G
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H
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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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R
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S
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T
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V
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W
A
AbstractCommand (class in hicstuff.commands)
add_cool_column() (in module hicstuff.io)
asd() (in module hicstuff.hicstuff)
attribute_fragments() (in module hicstuff.digest)
average_distance_law() (in module hicstuff.distance_law)
B
bin_annotation() (in module hicstuff.hicstuff)
bin_bp_dense() (in module hicstuff.hicstuff)
bin_bp_sparse() (in module hicstuff.hicstuff)
bin_dense() (in module hicstuff.hicstuff)
bin_exact_bp_dense() (in module hicstuff.hicstuff)
bin_matrix() (in module hicstuff.hicstuff)
bin_measurement() (in module hicstuff.hicstuff)
bin_sparse() (in module hicstuff.hicstuff)
build_pyramid() (in module hicstuff.hicstuff)
C
check_fasta_index() (in module hicstuff.io)
check_is_fasta() (in module hicstuff.io)
check_output_path() (hicstuff.commands.AbstractCommand method)
circular_distance_law() (in module hicstuff.distance_law)
compartments() (in module hicstuff.hicstuff)
compartments_sparse() (in module hicstuff.hicstuff)
contigs_to_positions() (in module hicstuff.hicstuff)
Convert (class in hicstuff.commands)
corrcoef_sparse() (in module hicstuff.hicstuff)
Cutsite (class in hicstuff.commands)
D
dade_to_graal() (in module hicstuff.io)
data_transform() (hicstuff.commands.View method)
despeckle_local() (in module hicstuff.hicstuff)
despeckle_simple() (in module hicstuff.hicstuff)
Digest (class in hicstuff.commands)
directional() (in module hicstuff.hicstuff)
distance_diagonal_law() (in module hicstuff.hicstuff)
distance_law() (in module hicstuff.hicstuff)
distance_law_from_mat() (in module hicstuff.hicstuff)
distance_to_contact() (in module hicstuff.hicstuff)
Distancelaw (class in hicstuff.commands)
domainogram() (in module hicstuff.hicstuff)
E
estimate_param_rippe() (in module hicstuff.hicstuff)
execute() (hicstuff.commands.AbstractCommand method)
(hicstuff.commands.Convert method)
(hicstuff.commands.Cutsite method)
(hicstuff.commands.Digest method)
(hicstuff.commands.Distancelaw method)
(hicstuff.commands.Filter method)
(hicstuff.commands.Iteralign method)
(hicstuff.commands.Missview method)
(hicstuff.commands.Pipeline method)
(hicstuff.commands.Rebin method)
(hicstuff.commands.Scalogram method)
(hicstuff.commands.Subsample method)
(hicstuff.commands.View method)
export_distance_law() (in module hicstuff.distance_law)
F
Filter (class in hicstuff.commands)
filter_bamfile() (in module hicstuff.iteralign)
filter_events() (in module hicstuff.filter)
find_frag() (in module hicstuff.digest)
flatten_positions_to_contigs() (in module hicstuff.hicstuff)
flexible_hic_loader() (in module hicstuff.io)
flexible_hic_saver() (in module hicstuff.io)
frag_len() (in module hicstuff.digest)
from_dade_matrix() (in module hicstuff.io)
from_structure() (in module hicstuff.hicstuff)
G
gc_bins() (in module hicstuff.io)
GC_partial() (in module hicstuff.hicstuff)
GC_wide() (in module hicstuff.hicstuff)
gen_enzyme_religation_regex() (in module hicstuff.digest)
generate_temp_dir() (in module hicstuff.io)
get_chr_segment_bins_index() (in module hicstuff.distance_law)
get_chr_segment_length() (in module hicstuff.distance_law)
get_distance_law() (in module hicstuff.distance_law)
get_good_bins() (in module hicstuff.hicstuff)
get_hic_format() (in module hicstuff.io)
get_missing_bins() (in module hicstuff.hicstuff)
get_names() (in module hicstuff.distance_law)
get_pairs_distance() (in module hicstuff.distance_law)
get_pairs_header() (in module hicstuff.io)
get_pos_cols() (in module hicstuff.io)
get_restriction_table() (in module hicstuff.digest)
get_thresholds() (in module hicstuff.filter)
get_ylim() (in module hicstuff.distance_law)
getrandbits() (in module hicstuff.io)
H
hicstuff (module)
hicstuff.commands (module)
hicstuff.digest (module)
hicstuff.distance_law (module)
hicstuff.filter (module)
hicstuff.hicstuff (module)
hicstuff.io (module)
hicstuff.iteralign (module)
hicstuff.main (module)
hicstuff.version (module)
hicstuff.view (module)
I
import_distance_law() (in module hicstuff.distance_law)
is_compressed() (in module hicstuff.io)
Iteralign (class in hicstuff.commands)
iterative_align() (in module hicstuff.iteralign)
L
largest_connected_component() (in module hicstuff.hicstuff)
load_bedgraph2d() (in module hicstuff.io)
load_cool() (in module hicstuff.io)
load_from_redis() (in module hicstuff.io)
load_into_redis() (in module hicstuff.io)
load_pos_col() (in module hicstuff.io)
load_sparse_matrix() (in module hicstuff.io)
logbins_xs() (in module hicstuff.distance_law)
M
mad() (in module hicstuff.hicstuff)
main() (in module hicstuff.main)
matrix_to_pdb() (in module hicstuff.hicstuff)
Missview (class in hicstuff.commands)
model_norm() (in module hicstuff.hicstuff)
N
noise() (in module hicstuff.hicstuff)
normalize() (in module hicstuff.view)
normalize_dense() (in module hicstuff.hicstuff)
normalize_distance_law() (in module hicstuff.distance_law)
normalize_sparse() (in module hicstuff.hicstuff)
null_model() (in module hicstuff.hicstuff)
P
parse_bin_str() (in module hicstuff.commands)
parse_ucsc() (in module hicstuff.commands)
pdb_to_structure() (in module hicstuff.hicstuff)
Pipeline (class in hicstuff.commands)
plot_matrix() (in module hicstuff.view)
plot_ps_slope() (in module hicstuff.distance_law)
positions_to_contigs() (in module hicstuff.hicstuff)
process_matrix() (hicstuff.commands.View method)
process_read_pair() (in module hicstuff.filter)
R
read_compressed() (in module hicstuff.io)
Rebin (class in hicstuff.commands)
remove_inter() (in module hicstuff.hicstuff)
remove_intra() (in module hicstuff.hicstuff)
rename_genome() (in module hicstuff.io)
reorder_fasta() (in module hicstuff.io)
(in module hicstuff.view)
rippe_parameters() (in module hicstuff.hicstuff)
S
save_bedgraph2d() (in module hicstuff.io)
save_cool() (in module hicstuff.io)
save_sparse_matrix() (in module hicstuff.io)
scaffold_distribution() (in module hicstuff.view)
Scalogram (class in hicstuff.commands)
scalogram() (in module hicstuff.hicstuff)
shortest_path_interpolation() (in module hicstuff.hicstuff)
simple_distance_diagonal_law() (in module hicstuff.hicstuff)
slope_distance_law() (in module hicstuff.distance_law)
sort_pairs() (in module hicstuff.io)
sparse_to_dense() (in module hicstuff.view)
split_genome() (in module hicstuff.hicstuff)
split_matrix() (in module hicstuff.hicstuff)
Subsample (class in hicstuff.commands)
subsample_contacts() (in module hicstuff.hicstuff)
sum_mat_bins() (in module hicstuff.hicstuff)
T
to_dade_matrix() (in module hicstuff.io)
to_distance() (in module hicstuff.hicstuff)
to_pdb() (in module hicstuff.hicstuff)
to_structure() (in module hicstuff.hicstuff)
trim_dense() (in module hicstuff.hicstuff)
trim_sparse() (in module hicstuff.hicstuff)
trim_structure() (in module hicstuff.hicstuff)
truncate_reads() (in module hicstuff.iteralign)
V
View (class in hicstuff.commands)
W
write_frag_info() (in module hicstuff.digest)
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