Bio2BEL
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Sources
How to Make a Bio2BEL Package
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Input and Output
Using the CLI
Reference
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Utilities
Testing
Bio2BEL
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Index
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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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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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W
Symbols
--connection <connection>
bio2bel-actions command line option
bio2bel-bel-write command line option
bio2bel-belns-write command line option
bio2bel-drop command line option
bio2bel-main command line option
bio2bel-populate command line option
bio2bel-sheet command line option
bio2bel-summarize command line option
bio2bel-web command line option
--debug
bio2bel-main-web command line option
--directory <directory>
bio2bel-bel-write command line option
bio2bel-belns-write command line option
bio2bel-er command line option
bio2bel-main-bel-write-edgelist command line option
bio2bel-main-belns-write command line option
bio2bel-main-export-gene-sets command line option
--file <file>
bio2bel-sheet command line option
--fmt <fmt>
bio2bel-main-export-gene-sets command line option
--force
bio2bel-bel-write command line option
bio2bel-belns-write command line option
bio2bel-main-populate command line option
bio2bel-populate command line option
--host <host>
bio2bel-main-bel-upload command line option
bio2bel-main-web command line option
bio2bel-web command line option
--index
bio2bel-sheet command line option
--output <output>
bio2bel-main-bel-write command line option
--port <port>
bio2bel-main-web command line option
bio2bel-web command line option
--reset
bio2bel-main-populate command line option
bio2bel-populate command line option
--secret-key <secret_key>
bio2bel-main-web command line option
--skip <skip>
bio2bel-bel-write command line option
bio2bel-belns-write command line option
bio2bel-cache-clear command line option
bio2bel-drop command line option
bio2bel-populate command line option
bio2bel-sheet command line option
bio2bel-summarize command line option
--tablefmt <tablefmt>
bio2bel-sheet command line option
--update
bio2bel-main-belns-upload command line option
--verbose
bio2bel-main-bel-upload command line option
bio2bel-main-bel-write command line option
bio2bel-main-bel-write-edgelist command line option
bio2bel-main-cache-clear command line option
bio2bel-main-cache-locate command line option
bio2bel-main-cache-ls command line option
bio2bel-main-drop command line option
bio2bel-main-populate command line option
bio2bel-main-summarize command line option
--yes
bio2bel-main-drop command line option
-c
bio2bel-actions command line option
bio2bel-bel-write command line option
bio2bel-belns-write command line option
bio2bel-drop command line option
bio2bel-main command line option
bio2bel-populate command line option
bio2bel-sheet command line option
bio2bel-summarize command line option
bio2bel-web command line option
-d
bio2bel-bel-write command line option
bio2bel-belns-write command line option
bio2bel-er command line option
bio2bel-main-bel-write-edgelist command line option
bio2bel-main-belns-write command line option
bio2bel-main-export-gene-sets command line option
-f
bio2bel-belns-write command line option
bio2bel-main-export-gene-sets command line option
bio2bel-main-populate command line option
bio2bel-sheet command line option
-h
bio2bel-main-web command line option
-k
bio2bel-main-web command line option
-o
bio2bel-main-bel-write command line option
-p
bio2bel-main-web command line option
-r
bio2bel-main-populate command line option
-s
bio2bel-bel-write command line option
bio2bel-belns-write command line option
bio2bel-cache-clear command line option
bio2bel-drop command line option
bio2bel-populate command line option
bio2bel-sheet command line option
bio2bel-summarize command line option
-u
bio2bel-main-belns-upload command line option
-v
bio2bel-main-bel-upload command line option
bio2bel-main-bel-write command line option
bio2bel-main-bel-write-edgelist command line option
bio2bel-main-cache-clear command line option
bio2bel-main-cache-locate command line option
bio2bel-main-cache-ls command line option
bio2bel-main-drop command line option
bio2bel-main-populate command line option
bio2bel-main-summarize command line option
bio2bel-main-web command line option
A
AbstractManager (class in bio2bel)
AbstractTemporaryCacheClassMixin (class in bio2bel.testing)
AbstractTemporaryCacheMethodMixin (class in bio2bel.testing)
Action (class in bio2bel.models)
add_namespace_to_graph() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method)
B
BELManagerMixin (class in bio2bel.manager.bel_manager)
BELNamespaceManagerMixin (class in bio2bel.manager.namespace_manager)
bio2bel
module
bio2bel-actions command line option
--connection <connection>
-c
bio2bel-bel-write command line option
--connection <connection>
--directory <directory>
--force
--skip <skip>
-c
-d
-s
bio2bel-belns-write command line option
--connection <connection>
--directory <directory>
--force
--skip <skip>
-c
-d
-f
-s
bio2bel-cache-clear command line option
--skip <skip>
-s
bio2bel-drop command line option
--connection <connection>
--skip <skip>
-c
-s
Drop all?
bio2bel-er command line option
--directory <directory>
-d
bio2bel-install command line option
NAME
bio2bel-main command line option
--connection <connection>
-c
bio2bel-main-bel-upload command line option
--host <host>
--verbose
-v
bio2bel-main-bel-write command line option
--output <output>
--verbose
-o
-v
bio2bel-main-bel-write-edgelist command line option
--directory <directory>
--verbose
-d
-v
bio2bel-main-belns-upload command line option
--update
-u
bio2bel-main-belns-write command line option
--directory <directory>
-d
bio2bel-main-cache-clear command line option
--verbose
-v
bio2bel-main-cache-locate command line option
--verbose
-v
bio2bel-main-cache-ls command line option
--verbose
-v
bio2bel-main-drop command line option
--verbose
--yes
-v
bio2bel-main-export-gene-sets command line option
--directory <directory>
--fmt <fmt>
-d
-f
bio2bel-main-populate command line option
--force
--reset
--verbose
-f
-r
-v
bio2bel-main-summarize command line option
--verbose
-v
bio2bel-main-web command line option
--debug
--host <host>
--port <port>
--secret-key <secret_key>
-h
-k
-p
-v
bio2bel-populate command line option
--connection <connection>
--force
--reset
--skip <skip>
-c
-s
bio2bel-sheet command line option
--connection <connection>
--file <file>
--index
--skip <skip>
--tablefmt <tablefmt>
-c
-f
-s
bio2bel-summarize command line option
--connection <connection>
--skip <skip>
-c
-s
bio2bel-web command line option
--connection <connection>
--host <host>
--port <port>
-c
bio2bel.downloading
module
bio2bel.io.automate
module
bio2bel.io.pykeen
module
bio2bel.models
module
bio2bel.sources.biogrid
module
bio2bel.sources.intact
module
bio2bel.sources.pid
module
bio2bel.sources.tfregulons
module
bio2bel.testing
module
bio2bel.utils
module
C
clear_cache() (in module bio2bel.utils)
connection() (bio2bel.AbstractManager property)
count() (bio2bel.models.Action class method)
count_relations() (bio2bel.manager.bel_manager.BELManagerMixin method)
create_all() (bio2bel.AbstractManager method)
(in module bio2bel.models)
created (bio2bel.models.Action attribute)
D
Drop all?
bio2bel-drop command line option
drop_all() (bio2bel.AbstractManager method)
drop_bel_namespace() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method)
E
enrich_graph() (in module bio2bel.sources.tfregulons)
ensure_bio2bel_installation() (in module bio2bel.io.automate)
ensure_graph() (in module bio2bel.io.automate)
ensure_path() (in module bio2bel.utils)
ensure_triples() (in module bio2bel.io.pykeen)
ensure_tsv() (in module bio2bel.io.automate)
entrez_id (bio2bel.sources.pid.Protein attribute)
F
flask_admin_models (bio2bel.manager.flask_manager.FlaskMixin attribute)
FlaskMixin (class in bio2bel.manager.flask_manager)
G
get_bel() (in module bio2bel.sources.biogrid)
(in module bio2bel.sources.intact)
(in module bio2bel.sources.tfregulons)
get_bio2bel_modules() (in module bio2bel.utils)
get_cli() (bio2bel.AbstractManager class method)
(bio2bel.manager.bel_manager.BELManagerMixin class method)
(bio2bel.manager.flask_manager.FlaskMixin class method)
(bio2bel.manager.namespace_manager.BELNamespaceManagerMixin class method)
get_connection() (in module bio2bel.utils)
get_data_dir() (in module bio2bel.utils)
get_df() (in module bio2bel.sources.tfregulons)
get_flask_admin_app() (bio2bel.manager.flask_manager.FlaskMixin method)
get_graph_from_cx() (in module bio2bel.sources.pid)
get_hgnc_ids() (in module bio2bel.sources.tfregulons)
get_namespace_hash() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method)
H
has_names (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin attribute)
hgnc_id (bio2bel.sources.pid.Protein attribute)
hgnc_symbol (bio2bel.sources.pid.Protein attribute)
I
identifier (bio2bel.sources.pid.Pathway attribute)
is_populated() (bio2bel.AbstractManager method)
iterate_graphs() (in module bio2bel.sources.pid)
L
ls() (bio2bel.models.Action class method)
M
make_df_getter() (in module bio2bel.downloading)
make_downloader() (in module bio2bel.downloading)
make_drop() (bio2bel.models.Action static method)
make_json_getter() (in module bio2bel.downloading)
make_populate() (bio2bel.models.Action static method)
make_populate_failed() (bio2bel.models.Action static method)
make_temporary_cache_class_mixin() (in module bio2bel.testing)
make_zipped_df_getter() (in module bio2bel.downloading)
Manager (class in bio2bel.sources.pid)
MockConnectionMixin (class in bio2bel.testing)
module
bio2bel
bio2bel.downloading
bio2bel.io.automate
bio2bel.io.pykeen
bio2bel.models
bio2bel.sources.biogrid
bio2bel.sources.intact
bio2bel.sources.pid
bio2bel.sources.tfregulons
bio2bel.testing
bio2bel.utils
N
NAME
bio2bel-install command line option
name (bio2bel.sources.pid.Pathway attribute)
namespace_model (bio2bel.sources.pid.Manager attribute)
P
Pathway (class in bio2bel.sources.pid)
pathway_model (bio2bel.sources.pid.Manager attribute)
populate() (bio2bel.AbstractManager method)
(bio2bel.sources.pid.Manager method)
(bio2bel.testing.AbstractTemporaryCacheClassMixin class method)
(bio2bel.testing.AbstractTemporaryCacheMethodMixin method)
prefix_directory_join() (in module bio2bel.utils)
Protein (class in bio2bel.sources.pid)
protein_model (bio2bel.sources.pid.Manager attribute)
R
resource (bio2bel.models.Action attribute)
S
setUp() (bio2bel.testing.AbstractTemporaryCacheMethodMixin method)
(bio2bel.testing.MockConnectionMixin method)
(bio2bel.testing.TemporaryConnectionMethodMixin method)
setUpClass() (bio2bel.testing.AbstractTemporaryCacheClassMixin class method)
(bio2bel.testing.TemporaryConnectionMixin class method)
store_drop() (bio2bel.models.Action class method)
store_populate() (bio2bel.models.Action class method)
store_populate_failed() (bio2bel.models.Action class method)
summarize() (bio2bel.AbstractManager method)
T
tearDown() (bio2bel.testing.AbstractTemporaryCacheMethodMixin method)
(bio2bel.testing.TemporaryConnectionMethodMixin method)
tearDownClass() (bio2bel.testing.AbstractTemporaryCacheClassMixin class method)
(bio2bel.testing.TemporaryConnectionMixin class method)
TemporaryConnectionMethodMixin (class in bio2bel.testing)
TemporaryConnectionMixin (class in bio2bel.testing)
to_bel() (bio2bel.manager.bel_manager.BELManagerMixin method)
to_indra_statements() (bio2bel.manager.bel_manager.BELManagerMixin method)
to_pybel() (bio2bel.sources.pid.Protein method)
U
upload_bel_namespace() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method)
W
write_bel_annotation() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method)
write_bel_namespace() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method)
write_bel_namespace_mappings() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method)
write_directory() (bio2bel.manager.namespace_manager.BELNamespaceManagerMixin method)
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