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Utils
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Index
Symbols
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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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W
Symbols
--connection <connection>
compath-drop command line option
compath-drop-databases command line option
compath-load-hierarchies command line option
compath-load-mappings command line option
compath-manage command line option
compath-populate command line option
compath-web command line option
--debug
compath-drop command line option
compath-drop-databases command line option
compath-populate command line option
compath-web command line option
--delete-first
compath-populate command line option
--email <email>
compath-load-hierarchies command line option
--host <host>
compath-web command line option
--port <port>
compath-web command line option
--static-folder <static_folder>
compath-web command line option
--template-folder <template_folder>
compath-web command line option
--yes
compath-drop command line option
compath-drop-databases command line option
-c
compath-drop command line option
compath-drop-databases command line option
compath-load-hierarchies command line option
compath-load-mappings command line option
compath-manage command line option
compath-populate command line option
compath-web command line option
-d
compath-populate command line option
-e
compath-load-hierarchies command line option
-v
compath-drop command line option
compath-drop-databases command line option
compath-populate command line option
compath-web command line option
-y
compath-drop command line option
compath-drop-databases command line option
A
accept_mapping() (compath.manager.Manager method)
accepted (compath.models.PathwayMapping attribute)
add_mapping_node() (in module compath.visualization.d3_dendrogram)
add_node() (in module compath.visualization.d3_dendrogram)
apply_filter() (in module compath.utils)
B
BLACK_LIST (in module compath.constants)
C
calculate_relative_enrichments() (in module compath.utils)
calculate_similarity() (in module compath.utils)
calculate_szymkiewicz_simpson_coefficient() (in module compath.utils)
claim_mapping() (compath.manager.Manager method)
compath
module
compath-drop command line option
--connection <connection>
--debug
--yes
-c
-v
-y
compath-drop-databases command line option
--connection <connection>
--debug
--yes
-c
-v
-y
compath-load-hierarchies command line option
--connection <connection>
--email <email>
-c
-e
compath-load-mappings command line option
--connection <connection>
-c
compath-manage command line option
--connection <connection>
-c
compath-manage-users-make-admin command line option
EMAIL
compath-manage-users-make-user command line option
EMAIL
PASSWORD
compath-populate command line option
--connection <connection>
--debug
--delete-first
-c
-d
-v
compath-web command line option
--connection <connection>
--debug
--host <host>
--port <port>
--static-folder <static_folder>
--template-folder <template_folder>
-c
-v
compath.constants
module
compath.curation.hierarchies
module
compath.curation.parser
module
compath.curation.utils
module
compath.manager
module
compath.models
module
compath.utils
module
compath.visualization.cytoscape
module
compath.visualization.d3_dendrogram
module
compath.visualization.venn_diagram
module
compath.web
module
ComPathSQLAlchemy (class in compath.web)
count_creators() (compath.models.PathwayMapping property)
count_down_votes() (compath.models.PathwayMapping property)
count_genes_in_pathway() (in module compath.utils)
count_mapping_user() (compath.manager.Manager method)
count_mappings() (compath.manager.Manager method)
count_up_votes() (compath.models.PathwayMapping property)
count_users() (compath.manager.Manager method)
count_votes() (compath.manager.Manager method)
(compath.models.PathwayMapping property)
create_all() (compath.manager.Manager method)
create_app() (in module compath.web)
create_hierarchical_mappings() (in module compath.curation.hierarchies)
create_similarity_matrix() (in module compath.visualization.d3_dendrogram)
D
delete_all_mappings() (compath.manager.Manager method)
delete_mapping_by_id() (compath.manager.Manager method)
dict_to_pandas_df() (in module compath.utils)
drop_all() (compath.manager.Manager method)
E
EMAIL
compath-manage-users-make-admin command line option
compath-manage-users-make-user command line option
enrich_graph_with_mappings() (in module compath.visualization.cytoscape)
EQUIVALENT_TO (in module compath.constants)
F
filter_network_by_similarity() (in module compath.visualization.cytoscape)
filter_results() (in module compath.utils)
from_connection() (compath.manager.Manager static method)
G
get_all_accepted_mappings() (compath.manager.Manager method)
get_all_mappings() (compath.manager.Manager method)
get_all_mappings_from_pathway() (compath.manager.Manager method)
get_all_pathways_from_db_with_mappings() (compath.manager.Manager method)
get_ancestry_mappings_from_pathway_with_is_part_of_relationship() (compath.manager.Manager method)
get_complement_mapping_info() (compath.models.PathwayMapping method)
get_decendents_mappings_from_pathway_with_is_part_of_relationship() (compath.manager.Manager method)
get_dendrogram_tree() (in module compath.visualization.d3_dendrogram)
get_descendants() (in module compath.visualization.d3_dendrogram)
get_enriched_pathways() (in module compath.utils)
get_gene_pathways() (in module compath.utils)
get_gene_sets_from_pathway_names() (in module compath.utils)
get_genes_without_assigned_pathways() (in module compath.utils)
get_last_action_in_module() (in module compath.utils)
get_mapping() (compath.manager.Manager method)
get_mapping_by_id() (compath.manager.Manager method)
get_mapping_dendrogram() (in module compath.visualization.d3_dendrogram)
get_mappings() (in module compath.utils)
get_mappings_by_type() (compath.manager.Manager method)
get_mappings_from_pathway_with_relationship() (compath.manager.Manager method)
get_most_similar_names() (in module compath.utils)
get_or_create_mapping() (compath.manager.Manager method)
get_or_create_vote() (compath.manager.Manager method)
get_pathway_info() (in module compath.utils)
get_pathway_model_by_id() (in module compath.utils)
get_pathway_model_by_name() (in module compath.utils)
get_pathways_from_statement() (in module compath.curation.utils)
get_top_matches() (in module compath.utils)
get_user_by_email() (compath.manager.Manager method)
get_user_vote() (compath.models.PathwayMapping method)
get_users_from_emails() (in module compath.curation.parser)
get_vote() (compath.manager.Manager method)
get_vote_by_id() (compath.manager.Manager method)
H
has_ancestry_pathway_tuple() (compath.models.PathwayMapping static method)
has_database_pathway() (compath.models.PathwayMapping static method)
has_descendant_pathway_tuple() (compath.models.PathwayMapping static method)
has_pathway() (compath.models.PathwayMapping static method)
has_pathway_tuple() (compath.models.PathwayMapping static method)
HIERARCHY_MANAGERS (in module compath.constants)
I
infer_hierarchy() (compath.manager.Manager method)
init_app() (compath.web.ComPathSQLAlchemy method)
is_acceptable() (compath.models.PathwayMapping property)
is_admin() (compath.models.User property)
is_valid_pathway_by_id() (in module compath.curation.utils)
is_valid_pathway_name() (in module compath.curation.utils)
K
KEGG (in module compath.constants)
KEGG_GENE_SET (in module compath.constants)
KEGG_URL (in module compath.constants)
L
label_tree() (in module compath.visualization.d3_dendrogram)
load_hierarchy() (in module compath.curation.hierarchies)
log (in module compath.utils)
M
Manager (class in compath.manager)
MAPPING_TYPES (in module compath.constants)
module
compath
compath.constants
compath.curation.hierarchies
compath.curation.parser
compath.curation.utils
compath.manager
compath.models
compath.utils
compath.visualization.cytoscape
compath.visualization.d3_dendrogram
compath.visualization.venn_diagram
compath.web
MSIG (in module compath.constants)
MSIG_GENE_SET (in module compath.constants)
N
networkx_to_cytoscape_js() (in module compath.visualization.cytoscape)
P
parse_curation_template() (in module compath.curation.parser)
parse_special_mappings() (in module compath.curation.parser)
PASSWORD
compath-manage-users-make-user command line option
PathwayMapping (class in compath.models)
pathways_to_similarity_network() (in module compath.visualization.cytoscape)
perform_hypergeometric_test() (in module compath.utils)
process_form_gene_set() (in module compath.utils)
process_overlap_for_venn_diagram() (in module compath.visualization.venn_diagram)
R
REACTOME (in module compath.constants)
REACTOME_GENE_SET (in module compath.constants)
REACTOME_URL (in module compath.constants)
remove_star_from_pathway_name() (in module compath.curation.utils)
Role (class in compath.models)
S
service_1_name (compath.models.PathwayMapping attribute)
service_1_pathway_id (compath.models.PathwayMapping attribute)
service_1_pathway_name (compath.models.PathwayMapping attribute)
service_2_name (compath.models.PathwayMapping attribute)
service_2_pathway_id (compath.models.PathwayMapping attribute)
service_2_pathway_name (compath.models.PathwayMapping attribute)
simulate_pathway_enrichment() (in module compath.utils)
STYLED_NAMES (in module compath.constants)
T
to_csv() (in module compath.utils)
type (compath.models.PathwayMapping attribute)
(compath.models.Vote attribute)
U
User (class in compath.models)
V
Vote (class in compath.models)
VOTE_ACCEPTANCE (in module compath.constants)
W
WIKIPATHWAYS (in module compath.constants)
WIKIPATHWAYS_GENE_SET (in module compath.constants)
WIKIPATHWAYS_URL (in module compath.constants)
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