TF-COMB
latest
Install
Examples
Methods
API reference
Changelog
TF-COMB
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
W
A
add_object() (tfcomb.objects.DiffCombObj method)
add_region_overlap() (in module tfcomb.utils)
analyze_distances() (tfcomb.objects.CombObj method)
analyze_hubs() (tfcomb.objects.DistObj method)
analyze_orientation() (tfcomb.objects.CombObj method)
analyze_signal_all() (tfcomb.objects.DistObj method)
analyze_signal_chunks() (in module tfcomb.utils)
annotate_regions() (in module tfcomb.annotation)
append() (tfcomb.utils.TFBSPairList method)
as_table() (tfcomb.utils.TFBSPairList method)
aspect_translation (tfcomb.annotation.GOAnalysis attribute)
B
bigwig_path (tfcomb.utils.TFBSPairList property)
bubble() (in module tfcomb.plotting)
build_network() (in module tfcomb.network)
(tfcomb.objects.CombObj method)
(tfcomb.objects.DistObj method)
C
calculate_background() (in module tfcomb.utils)
calculate_foldchanges() (tfcomb.objects.DiffCombObj method)
calculate_TFBS() (in module tfcomb.utils)
check_boundaries() (in module tfcomb.utils)
check_columns() (in module tfcomb.utils)
check_datasource() (tfcomb.objects.DistObj method)
check_dir() (in module tfcomb.utils)
check_graphtool() (in module tfcomb.utils)
check_min_max_dist() (tfcomb.objects.DistObj method)
check_module() (in module tfcomb.utils)
check_pair() (tfcomb.objects.CombObj method)
check_peaks() (tfcomb.objects.DistObj method)
check_string() (in module tfcomb.utils)
check_type() (in module tfcomb.utils)
check_value() (in module tfcomb.utils)
check_writeability() (in module tfcomb.utils)
chunk_table() (tfcomb.objects.DistObj static method)
classify_rules() (tfcomb.objects.DistObj method)
clear() (tfcomb.utils.TFBSPairList method)
cluster_blockmodel() (in module tfcomb.network)
cluster_louvain() (in module tfcomb.network)
cluster_network() (tfcomb.objects.CombObj method)
cluster_TFBS() (tfcomb.objects.CombObj method)
CombObj (class in tfcomb.objects)
comp_plotting_tables() (tfcomb.utils.TFBSPairList method)
compare() (tfcomb.annotation.GOAnalysis method)
(tfcomb.objects.CombObj method)
copy() (tfcomb.objects.CombObj method)
correct_background() (tfcomb.objects.DistObj method)
count_distances() (tfcomb.objects.DistObj method)
count_peaks() (tfcomb.objects.DistObj method)
count_within() (tfcomb.objects.CombObj method)
create_distObj() (tfcomb.objects.CombObj method)
create_random_network() (in module tfcomb.network)
D
DiffCombObj (class in tfcomb.objects)
DistObj (class in tfcomb.objects)
E
enrichment() (tfcomb.annotation.GOAnalysis method)
evaluate_noise() (tfcomb.objects.DistObj method)
evaluate_noise_chunks() (in module tfcomb.utils)
extend() (tfcomb.utils.TFBSPairList method)
F
fill_rules() (tfcomb.objects.DistObj method)
from_pickle() (tfcomb.objects.CombObj method)
(tfcomb.objects.DiffCombObj method)
G
genome_view() (in module tfcomb.plotting)
get_annotated_genes() (in module tfcomb.annotation)
get_betweenness_centrality() (in module tfcomb.network)
get_degree() (in module tfcomb.network)
get_edge_table() (in module tfcomb.network)
get_node_table() (in module tfcomb.network)
get_pair_locations() (tfcomb.objects.CombObj method)
get_periodicity() (tfcomb.objects.DistObj method)
get_threshold() (in module tfcomb.utils)
getAllAttr() (in module tfcomb.utils)
go_bubble() (in module tfcomb.plotting)
GOAnalysis (class in tfcomb.annotation)
H
heatmap() (in module tfcomb.plotting)
I
InputError
insert() (tfcomb.utils.TFBSPairList method)
integrate_data() (tfcomb.objects.CombObj method)
is_smoothed() (tfcomb.objects.DistObj method)
is_symmetric() (in module tfcomb.utils)
L
log_progress() (in module tfcomb.utils)
M
make_symmetric() (in module tfcomb.utils)
market_basket() (tfcomb.objects.CombObj method)
max_distance() (tfcomb.objects.DistObj method)
mean_distance() (tfcomb.objects.DistObj method)
module
tfcomb.analysis
tfcomb.annotation
tfcomb.network
tfcomb.objects
tfcomb.plotting
tfcomb.utils
N
network() (in module tfcomb.plotting)
normalize() (tfcomb.objects.DiffCombObj method)
O
OneTFBS (class in tfcomb.utils)
open_bigwig() (in module tfcomb.utils)
open_genome() (in module tfcomb.utils)
orientation() (in module tfcomb.analysis)
OrientationAnalysis (class in tfcomb.analysis)
P
pairLines() (tfcomb.utils.TFBSPairList method)
pairMap() (tfcomb.utils.TFBSPairList method)
pairTrack() (tfcomb.utils.TFBSPairList method)
pairTrackAnimation() (tfcomb.utils.TFBSPairList method)
plot() (tfcomb.objects.DistObj method)
plot_autocorrelation() (tfcomb.objects.DistObj method)
plot_bg_estimation() (tfcomb.objects.DistObj method)
plot_bubble() (tfcomb.annotation.GOAnalysis method)
(tfcomb.objects.CombObj method)
(tfcomb.objects.DiffCombObj method)
plot_correlation() (tfcomb.objects.DiffCombObj method)
plot_distances() (tfcomb.utils.TFBSPairList method)
plot_heatmap() (tfcomb.analysis.OrientationAnalysis method)
(tfcomb.objects.CombObj method)
(tfcomb.objects.DiffCombObj method)
plot_network() (tfcomb.objects.CombObj method)
(tfcomb.objects.DiffCombObj method)
(tfcomb.objects.DistObj method)
plot_powerlaw() (in module tfcomb.network)
plot_rules_heatmap() (tfcomb.objects.DiffCombObj method)
plot_scatter() (tfcomb.objects.CombObj method)
plot_TFBS() (tfcomb.objects.CombObj method)
plotting_tables (tfcomb.utils.TFBSPairList property)
pop() (tfcomb.utils.TFBSPairList method)
prepare_motifs() (in module tfcomb.utils)
Progress (class in tfcomb.utils)
R
random_string() (in module tfcomb.utils)
rank_rules() (tfcomb.objects.DistObj method)
reduce_TFBS() (tfcomb.objects.CombObj method)
remove() (tfcomb.utils.TFBSPairList method)
reset_signal() (tfcomb.objects.DistObj method)
resolve_overlaps() (in module tfcomb.utils)
S
scale() (tfcomb.objects.DistObj method)
scatter() (in module tfcomb.plotting)
select_custom_rules() (tfcomb.objects.CombObj method)
select_rules() (tfcomb.objects.DiffCombObj method)
select_significant_rules() (tfcomb.objects.CombObj method)
select_TF_rules() (tfcomb.objects.CombObj method)
select_top_rules() (tfcomb.objects.CombObj method)
set_contrast() (in module tfcomb.utils)
set_orientation() (tfcomb.utils.TFBSPairList method)
set_prefix() (tfcomb.objects.CombObj method)
set_verbosity() (tfcomb.objects.CombObj method)
(tfcomb.objects.DistObj method)
shuffle_array() (in module tfcomb.utils)
shuffle_sites() (in module tfcomb.utils)
simplify_rules() (tfcomb.objects.CombObj method)
smooth() (tfcomb.objects.DistObj method)
StopExecution
subset_graph() (in module tfcomb.network)
subset_TFBS() (tfcomb.objects.CombObj method)
T
TFBS_from_bed() (tfcomb.objects.CombObj method)
TFBS_from_motifs() (tfcomb.objects.CombObj method)
TFBS_from_TOBIAS() (tfcomb.objects.CombObj method)
TFBS_to_bed() (tfcomb.objects.CombObj method)
TFBSPair (class in tfcomb.utils)
TFBSPairList (class in tfcomb.utils)
tfcomb.analysis
module
tfcomb.annotation
module
tfcomb.network
module
tfcomb.objects
module
tfcomb.plotting
module
tfcomb.utils
module
to_pickle() (tfcomb.objects.CombObj method)
(tfcomb.objects.DiffCombObj method)
U
unique_region_names() (in module tfcomb.utils)
W
write_bed() (tfcomb.utils.TFBSPairList method)
write_progress() (tfcomb.utils.Progress method)
Read the Docs
v: latest
Versions
latest
stable
Downloads
pdf
html
epub
On Read the Docs
Project Home
Builds