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DeepCpG 1.0.5 documentation
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A
acc() (in module deepcpg.evaluation)
add_output_layers() (in module deepcpg.models.utils)
add_to_dict() (in module deepcpg.data.utils)
annotate() (in module scripts.dcpg_eval_perf)
auc() (in module deepcpg.evaluation)
C
cat2_var() (in module deepcpg.data.stats)
cat_acc() (in module deepcpg.evaluation)
cat_var() (in module deepcpg.data.stats)
char_to_int() (in module deepcpg.data.dna)
CnnL1h128 (class in deepcpg.models.dna)
CnnL1h256 (class in deepcpg.models.dna)
CnnL2h128 (class in deepcpg.models.dna)
CnnL2h256 (class in deepcpg.models.dna)
CnnL3h128 (class in deepcpg.models.dna)
CnnL3h256 (class in deepcpg.models.dna)
CnnRnn01 (class in deepcpg.models.dna)
copy_weights() (in module deepcpg.models.utils)
cor() (in module deepcpg.evaluation)
CpgModel (class in deepcpg.models.cpg)
D
data_reader_from_model() (in module deepcpg.models.utils)
DataReader (class in deepcpg.models.utils)
decode_replicate_names() (in module deepcpg.models.utils)
deepcpg.callbacks (module)
deepcpg.data.annotations (module)
deepcpg.data.dna (module)
deepcpg.data.fasta (module)
deepcpg.data.feature_extractor (module)
deepcpg.data.hdf (module)
deepcpg.data.stats (module)
deepcpg.data.utils (module)
deepcpg.evaluation (module)
deepcpg.models.cpg (module)
deepcpg.models.dna (module)
deepcpg.models.utils (module)
deepcpg.motifs (module)
deepcpg.utils (module)
diff() (in module deepcpg.data.stats)
distance() (in module deepcpg.data.annotations)
DnaModel (class in deepcpg.models.dna)
E
encode_replicate_names() (in module deepcpg.models.utils)
entropy() (in module deepcpg.data.stats)
evaluate() (in module deepcpg.evaluation)
evaluate_cat() (in module deepcpg.evaluation)
evaluate_curve() (in module deepcpg.evaluation)
evaluate_generator() (in module deepcpg.models.utils)
evaluate_outputs() (in module deepcpg.evaluation)
extend_len() (in module deepcpg.data.annotations)
extend_len_frame() (in module deepcpg.data.annotations)
extract() (deepcpg.data.feature_extractor.KnnCpgFeatureExtractor method)
extract_seq_windows() (in module scripts.dcpg_data)
F
f1() (in module deepcpg.evaluation)
FastaSeq (class in deepcpg.data.fasta)
FcAvg (class in deepcpg.models.cpg)
filter_regex() (in module deepcpg.utils)
fold_dict() (in module deepcpg.utils)
format_chromo() (in module deepcpg.data.utils)
format_table() (in module deepcpg.utils)
format_table_row() (in module deepcpg.utils)
G
get() (in module deepcpg.data.stats)
(in module deepcpg.evaluation)
(in module deepcpg.models.cpg)
(in module deepcpg.models.dna)
get_alphabet() (in module deepcpg.data.dna)
get_anno_names() (in module deepcpg.data.utils)
get_cpg_wlen() (in module deepcpg.data.utils)
get_curve_fun() (in module scripts.dcpg_eval_perf)
get_dna_wlen() (in module deepcpg.data.utils)
get_first_conv_layer() (in module deepcpg.models.utils)
get_from_module() (in module deepcpg.utils)
get_nb_sample() (in module deepcpg.data.utils)
get_objectives() (in module deepcpg.models.utils)
get_output_metrics() (in module deepcpg.evaluation)
get_output_names() (in module deepcpg.data.utils)
get_replicate_names() (in module deepcpg.data.utils)
get_report() (in module deepcpg.motifs)
get_sample_weights() (in module deepcpg.models.utils)
group_overlapping() (in module deepcpg.data.annotations)
GzipFile (class in deepcpg.data.utils)
H
hnames_to_names() (in module deepcpg.data.hdf)
I
in_which() (in module deepcpg.data.annotations)
index_intervals() (deepcpg.data.feature_extractor.IntervalFeatureExtractor static method)
inputs() (deepcpg.models.utils.Model method)
int_to_char() (in module deepcpg.data.dna)
int_to_onehot() (in module deepcpg.data.dna)
IntervalFeatureExtractor (class in deepcpg.data.feature_extractor)
is_bedgraph() (in module deepcpg.data.utils)
is_binary() (in module deepcpg.data.utils)
is_binary_output() (in module deepcpg.evaluation)
is_in() (in module deepcpg.data.annotations)
J
join_intervals() (deepcpg.data.feature_extractor.IntervalFeatureExtractor static method)
join_overlapping() (in module deepcpg.data.annotations)
join_overlapping_frame() (in module deepcpg.data.annotations)
K
kendall() (in module deepcpg.evaluation)
KnnCpgFeatureExtractor (class in deepcpg.data.feature_extractor)
L
linear_weights() (in module deepcpg.utils)
list_models() (in module deepcpg.models.cpg)
(in module deepcpg.models.dna)
load_model() (in module deepcpg.models.utils)
ls() (in module deepcpg.data.hdf)
M
mad() (in module deepcpg.evaluation)
make_dir() (in module deepcpg.utils)
map_cpg_tables() (in module scripts.dcpg_data)
map_values() (in module scripts.dcpg_data)
mcc() (in module deepcpg.evaluation)
mean() (in module deepcpg.data.stats)
mode() (in module deepcpg.data.stats)
Model (class in deepcpg.models.utils)
move_columns_front() (in module deepcpg.utils)
mse() (in module deepcpg.evaluation)
O
onehot_to_int() (in module deepcpg.data.dna)
P
parse_lines() (in module deepcpg.data.fasta)
PerformanceLogger (class in deepcpg.callbacks)
predict_generator() (in module deepcpg.models.utils)
prepro_pos_table() (in module scripts.dcpg_data)
ProgressBar (class in deepcpg.utils)
R
read_anno_file() (in module scripts.dcpg_eval_perf)
read_bed() (in module deepcpg.data.annotations)
read_chromo() (in module deepcpg.data.fasta)
read_cpg_profile() (in module deepcpg.data.utils)
read_cpg_profiles() (in module scripts.dcpg_data)
read_file() (in module deepcpg.data.fasta)
read_from() (in module deepcpg.models.utils)
read_meme_db() (in module deepcpg.motifs)
read_tomtom() (in module deepcpg.motifs)
ResAtrous01 (class in deepcpg.models.dna)
ResConv01 (class in deepcpg.models.dna)
ResNet01 (class in deepcpg.models.dna)
ResNet02 (class in deepcpg.models.dna)
rmse() (in module deepcpg.evaluation)
RnnL1 (class in deepcpg.models.cpg)
RnnL2 (class in deepcpg.models.cpg)
S
sample_from_chromo() (in module deepcpg.data.utils)
save_model() (in module deepcpg.models.utils)
ScaledSigmoid (class in deepcpg.models.utils)
scripts.dcpg_data (module)
scripts.dcpg_data_show (module)
scripts.dcpg_data_stats (module)
scripts.dcpg_download (module)
scripts.dcpg_eval (module)
scripts.dcpg_eval_export (module)
scripts.dcpg_eval_perf (module)
scripts.dcpg_filter_act (module)
scripts.dcpg_filter_motifs (module)
scripts.dcpg_snp (module)
scripts.dcpg_train (module)
scripts.dcpg_train_viz (module)
search_model_files() (in module deepcpg.models.utils)
select_file_by_chromo() (in module deepcpg.data.fasta)
slice_dict() (in module deepcpg.utils)
split_ext() (in module scripts.dcpg_data)
stack_dict() (in module deepcpg.data.utils)
T
threadsafe_generator() (in module deepcpg.data.utils)
threadsafe_iter (class in deepcpg.data.utils)
tnr() (in module deepcpg.evaluation)
to_list() (in module deepcpg.utils)
tpr() (in module deepcpg.evaluation)
TrainingStopper (class in deepcpg.callbacks)
U
unstack_report() (in module deepcpg.evaluation)
V
var() (in module deepcpg.data.stats)
W
write_data() (in module deepcpg.data.hdf)
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DeepCpG 1.0.5 documentation
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