0.5.0
Main
Bridging the gap between data, methods and knowledge in the network inference field
Installation
API
Details
Data
Methods
Evaluation strategies
Contribution guidelines
General guidelines for contribution
Contribution’s guideline: Data
Contribution’s guideline: Methods
Contribution’s guideline: Evaluation strategies
Vignettes
Vignette 1: Introduction to NetworkCommons
Vignette 2: Using multiple methods to infer the networks
Vignette 3: Evaluating methods under two scenarios: offtarget recovery and pathway activity
Vignette 4: Sensitive response to drug perturbation using phosphoproteomics
Vignette 5: Multi-omics validation - Recovery of dysregulated kinases in response to cancer mutations
Additional resources
Vignette A: recursive propagation with MOON
Vignette B: Pertpy bridging to NetworkCommons
NetworkCommons
Index
Edit on GitHub
Index
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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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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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T
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U
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V
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Y
_
__init__() (networkcommons.visual.NetworkXVisualizer method)
(networkcommons.visual.YFilesVisualizer method)
A
add_pagerank_scores() (in module networkcommons.methods)
adjust_node_labels() (networkcommons.visual.NetworkXVisualizer method)
apply_edge_style() (in module networkcommons.visual)
apply_node_style() (in module networkcommons.visual)
B
build_heatmap_with_tree() (in module networkcommons.visual)
build_ma_plot() (in module networkcommons.visual)
build_volcano_plot() (in module networkcommons.visual)
C
color_by (networkcommons.visual.NetworkXVisualizer attribute)
color_edges() (networkcommons.visual.NetworkXVisualizer method)
,
[1]
color_nodes() (networkcommons.visual.NetworkXVisualizer method)
,
[1]
compress_same_children() (in module networkcommons.methods)
compute_all_paths() (in module networkcommons.methods)
compute_ppr_overlap() (in module networkcommons.methods)
convert_ensembl_to_gene_symbol() (in module networkcommons.data.omics)
cptac_cohortsize() (in module networkcommons.data.omics)
cptac_datatypes() (in module networkcommons.data.omics)
cptac_extend_dataframe() (in module networkcommons.data.omics)
cptac_fileinfo() (in module networkcommons.data.omics)
cptac_table() (in module networkcommons.data.omics)
create_heatmap() (in module networkcommons.visual)
custom_edge_color_mapping() (networkcommons.visual.YFilesVisualizer method)
(networkcommons.visual.YFilesVisualizer static method)
custom_factor_mapping() (networkcommons.visual.YFilesVisualizer method)
(networkcommons.visual.YFilesVisualizer static method)
custom_label_styles_mapping() (networkcommons.visual.YFilesVisualizer method)
(networkcommons.visual.YFilesVisualizer static method)
custom_node_color_mapping() (networkcommons.visual.YFilesVisualizer method)
(networkcommons.visual.YFilesVisualizer static method)
D
datasets() (in module networkcommons.data.omics)
decompress_moon_result() (in module networkcommons.methods)
decoupler_formatter() (in module networkcommons.utils)
decryptm_datasets() (in module networkcommons.data.omics)
decryptm_experiment() (in module networkcommons.data.omics)
decryptm_table() (in module networkcommons.data.omics)
deseq2() (in module networkcommons.data.omics)
E
edge_attrs_from_corneto() (in module networkcommons.utils)
edge_colors (networkcommons.visual.NetworkXVisualizer attribute)
F
filter_incoherent_TF_target() (in module networkcommons.methods)
filter_input_nodes_not_in_pkn() (in module networkcommons.methods)
filter_pkn_expressed_genes() (in module networkcommons.methods)
G
get_comparison_color() (in module networkcommons.visual)
get_connected_targets() (in module networkcommons.eval)
get_cosmos_pkn() (in module networkcommons.data.network)
get_ec50_evaluation() (in module networkcommons.eval)
get_edge_color() (in module networkcommons.visual)
get_ensembl_mappings() (in module networkcommons.data.omics)
get_graph_metrics() (in module networkcommons.eval)
get_lianaplus() (in module networkcommons.data.network)
get_mean_betweenness() (in module networkcommons.eval)
get_mean_closeness() (in module networkcommons.eval)
get_mean_degree() (in module networkcommons.eval)
get_metric_from_networks() (in module networkcommons.eval)
get_number_edges() (in module networkcommons.eval)
get_number_nodes() (in module networkcommons.eval)
get_omnipath() (in module networkcommons.data.network)
get_phosphorylation_status() (in module networkcommons.eval)
get_phosphositeplus() (in module networkcommons.data.network)
get_recovered_offtargets() (in module networkcommons.eval)
get_styles() (in module networkcommons.visual)
get_subnetwork() (in module networkcommons.utils)
H
handle_missing_values() (in module networkcommons.utils)
I
is_expressed() (in module networkcommons.methods)
K
keep_controllable_neighbours() (in module networkcommons.methods)
keep_observable_neighbours() (in module networkcommons.methods)
L
lollipop_plot() (in module networkcommons.visual)
M
merge_styles() (in module networkcommons.visual)
N
nci60_datasets() (in module networkcommons.data.omics)
nci60_datatypes() (in module networkcommons.data.omics)
nci60_table() (in module networkcommons.data.omics)
network (networkcommons.visual.YFilesVisualizer attribute)
network_from_df() (in module networkcommons.utils)
NetworkXVisualizer (class in networkcommons.visual)
node_attrs_from_corneto() (in module networkcommons.utils)
P
panacea_datatypes() (in module networkcommons.data.omics)
panacea_experiments() (in module networkcommons.data.omics)
panacea_gold_standard() (in module networkcommons.data.omics)
panacea_tables() (in module networkcommons.data.omics)
perform_random_controls() (in module networkcommons.eval)
phospho_egf_datatypes() (in module networkcommons.data.omics)
phospho_egf_tables() (in module networkcommons.data.omics)
plot_density() (in module networkcommons.visual)
plot_pca() (in module networkcommons.visual)
plot_rank() (in module networkcommons.visual)
plot_scatter() (in module networkcommons.visual)
prepare_metab_inputs() (in module networkcommons.methods)
R
read_network_from_file() (in module networkcommons.utils)
reduce_solution_network() (in module networkcommons.methods)
run_all_paths() (in module networkcommons.methods)
run_corneto_carnival() (in module networkcommons.methods)
run_moon_core() (in module networkcommons.methods)
run_ora() (in module networkcommons.eval)
run_reachability_filter() (in module networkcommons.methods)
run_shortest_paths() (in module networkcommons.methods)
run_sign_consistency() (in module networkcommons.methods)
run_signalingprofiler() (in module networkcommons.methods)
S
scperturb() (in module networkcommons.data.omics)
scperturb_datasets() (in module networkcommons.data.omics)
scperturb_metadata() (in module networkcommons.data.omics)
set_custom_edge_colors() (networkcommons.visual.NetworkXVisualizer method)
,
[1]
set_custom_style() (networkcommons.visual.NetworkXVisualizer method)
set_style_attributes() (in module networkcommons.visual)
shuffle_dict_keys() (in module networkcommons.eval)
styles (networkcommons.visual.YFilesVisualizer attribute)
subset_df_with_nodes() (in module networkcommons.utils)
T
targetlayer_formatter() (in module networkcommons.utils)
to_cornetograph() (in module networkcommons.utils)
to_networkx() (in module networkcommons.utils)
translate_res() (in module networkcommons.methods)
U
update_edge_property() (in module networkcommons.visual)
update_node_property() (in module networkcommons.visual)
V
vis_comparison() (networkcommons.visual.YFilesVisualizer method)
,
[1]
visualize() (networkcommons.visual.NetworkXVisualizer method)
,
[1]
(networkcommons.visual.YFilesVisualizer method)
,
[1]
visualize_network() (networkcommons.visual.NetworkXVisualizer method)
,
[1]
visualize_network_default() (networkcommons.visual.NetworkXVisualizer method)
,
[1]
visualize_network_sign_consistent() (networkcommons.visual.NetworkXVisualizer method)
,
[1]
visualize_network_simple() (networkcommons.visual.NetworkXVisualizer method)
Y
YFilesVisualizer (class in networkcommons.visual)