Orca
orca_predict module
orca_utils module
orca_models module
orca_modules module
selene_utils2 module
Orca
»
Index
Index
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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O
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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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V
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W
B
background_cis (selene_utils2.RandomPositionsSamplerHiC attribute)
background_trans (selene_utils2.RandomPositionsSamplerHiC attribute)
bg (selene_utils2.RandomPositionsSamplerHiC attribute)
bin_size (selene_utils2.MultibinGenomicFeatures attribute)
C
cg (selene_utils2.Genomic2DFeatures attribute)
chr() (orca_utils.GRange property)
chr_name (orca_utils.StructuralChange2 attribute)
chrs (selene_utils2.MemmapGenome attribute)
colormaps (module)
coord_clip() (in module orca_utils)
coord_points (orca_utils.StructuralChange2 attribute)
coord_round() (in module orca_utils)
cross_chromosome (selene_utils2.RandomPositionsSamplerHiC attribute)
D
data (selene_utils2.Genomic2DFeatures attribute)
(selene_utils2.MultibinGenomicFeatures attribute)
Decoder (class in orca_modules)
Decoder_1m (class in orca_modules)
delete() (orca_utils.StructuralChange2 method)
denets (orca_models.H1esc attribute)
(orca_models.H1esc_256M attribute)
(orca_models.HCTnoc attribute)
(orca_models.Hff attribute)
(orca_models.Hff_256M attribute)
duplicate() (orca_utils.StructuralChange2 method)
E
Encoder (class in orca_modules)
Encoder2 (class in orca_modules)
Encoder3 (class in orca_modules)
end() (orca_utils.GRange property)
epss (orca_models.H1esc attribute)
(orca_models.H1esc_1M attribute)
(orca_models.H1esc_256M attribute)
(orca_models.HCTnoc attribute)
(orca_models.Hff attribute)
(orca_models.Hff_1M attribute)
(orca_models.Hff_256M attribute)
F
feature_index_dict (selene_utils2.Genomic2DFeatures attribute)
(selene_utils2.MultibinGenomicFeatures attribute)
forward() (orca_models.H1esc_1M method)
(orca_models.Hff_1M method)
(orca_modules.Decoder method)
(orca_modules.Decoder_1m method)
(orca_modules.Encoder method)
(orca_modules.Encoder2 method)
(orca_modules.Encoder3 method)
(orca_modules.Net method)
G
genome (selene_utils2.MemmapGenome attribute)
genomeplot() (in module orca_utils)
genomeplot_256Mb() (in module orca_utils)
genomepredict() (in module orca_predict)
genomepredict_256Mb() (in module orca_predict)
Genomic2DFeatures (class in selene_utils2)
get_encoding_from_coords() (selene_utils2.MemmapGenome method)
get_encoding_from_coords_check_unk() (selene_utils2.MemmapGenome method)
get_feature_data() (selene_utils2.Genomic2DFeatures method)
(selene_utils2.MultibinGenomicFeatures method)
GRange (class in orca_utils)
H
H1esc (class in orca_models)
H1esc_1M (class in orca_models)
H1esc_256M (class in orca_models)
HCTnoc (class in orca_models)
Hff (class in orca_models)
Hff_1M (class in orca_models)
Hff_256M (class in orca_models)
I
index_feature_dict (selene_utils2.MultibinGenomicFeatures attribute)
indices() (selene_utils2.SampleIndices property)
init() (selene_utils2.MemmapGenome method)
(selene_utils2.MultibinGenomicFeatures method)
(selene_utils2.RandomPositionsSamplerHiC method)
insert() (orca_utils.StructuralChange2 method)
invert() (orca_utils.StructuralChange2 method)
L
len() (orca_utils.LGRange property)
len_chrs (selene_utils2.MemmapGenome attribute)
length_schedule (selene_utils2.RandomPositionsSamplerHiC attribute)
LGRange (class in orca_utils)
load_resources() (in module orca_predict)
M
max_seg_length (selene_utils2.RandomPositionsSamplerHiC attribute)
MemmapGenome (class in selene_utils2)
mode (selene_utils2.MultibinGenomicFeatures attribute)
(selene_utils2.RandomPositionsSamplerHiC attribute)
modes (selene_utils2.RandomPositionsSamplerHiC attribute)
MultibinGenomicFeatures (class in selene_utils2)
N
n_features (selene_utils2.Genomic2DFeatures attribute)
(selene_utils2.MultibinGenomicFeatures attribute)
Net (class in orca_modules)
net (orca_models.H1esc attribute)
(orca_models.H1esc_1M attribute)
(orca_models.H1esc_256M attribute)
(orca_models.HCTnoc attribute)
(orca_models.Hff attribute)
(orca_models.Hff_1M attribute)
(orca_models.Hff_256M attribute)
net0 (orca_models.H1esc attribute)
(orca_models.H1esc_256M attribute)
(orca_models.HCTnoc attribute)
(orca_models.Hff attribute)
(orca_models.Hff_256M attribute)
net1 (orca_models.H1esc_256M attribute)
(orca_models.Hff_256M attribute)
normmats (orca_models.H1esc attribute)
(orca_models.H1esc_1M attribute)
(orca_models.H1esc_256M attribute)
(orca_models.HCTnoc attribute)
(orca_models.Hff attribute)
(orca_models.Hff_1M attribute)
(orca_models.Hff_256M attribute)
O
orca_models (module)
orca_modules (module)
orca_predict (module)
orca_utils (module)
P
permute_segments (selene_utils2.RandomPositionsSamplerHiC attribute)
position_resolution (selene_utils2.RandomPositionsSamplerHiC attribute)
process_anno() (in module orca_utils)
process_custom() (in module orca_predict)
process_del() (in module orca_predict)
process_dup() (in module orca_predict)
process_ins() (in module orca_predict)
process_inv() (in module orca_predict)
process_region() (in module orca_predict)
process_single_breakpoint() (in module orca_predict)
Q
query() (orca_utils.StructuralChange2 method)
query_ref() (orca_utils.StructuralChange2 method)
R
random_shift (selene_utils2.RandomPositionsSamplerHiC attribute)
random_strand (selene_utils2.RandomPositionsSamplerHiC attribute)
RandomPositionsSamplerHiC (class in selene_utils2)
ref() (orca_utils.LGRange property)
reference_sequence (selene_utils2.RandomPositionsSamplerHiC attribute)
S
sample() (selene_utils2.RandomPositionsSamplerHiC method)
SampleIndices (class in selene_utils2)
segments (orca_utils.StructuralChange2 attribute)
selene_utils2 (module)
sequence_length (selene_utils2.RandomPositionsSamplerHiC attribute)
shape (selene_utils2.Genomic2DFeatures attribute)
(selene_utils2.MultibinGenomicFeatures attribute)
start() (orca_utils.GRange property)
step_size (selene_utils2.MultibinGenomicFeatures attribute)
strand() (orca_utils.GRange property)
StructuralChange2 (class in orca_utils)
T
target (selene_utils2.RandomPositionsSamplerHiC attribute)
target_1d (selene_utils2.RandomPositionsSamplerHiC attribute)
test_holdout (selene_utils2.RandomPositionsSamplerHiC attribute)
V
validation_holdout (selene_utils2.RandomPositionsSamplerHiC attribute)
W
weights() (selene_utils2.SampleIndices property)