API

Import Omnipath as:

import omnipath as op

Requests

requests.Annotations()

Request annotations from [OmniPath].

requests.Complexes()

Request information about protein complexes from [OmniPath].

requests.Enzsub()

Request enzyme-substrate relationships from [OmniPath].

requests.Intercell()

Request intercell annotations from [OmniPath].

requests.SignedPTMs()

Request enzyme-substrate relationships and interactions from [OmniPath].

Interactions

interactions.AllInteractions([include, exclude])

Request all [OmniPath] interaction datasets.

interactions.Dorothea()

Request interactions from the dorothea dataset.

interactions.KinaseExtra()

Request interactions from the kinase extra dataset.

interactions.LigRecExtra()

Request interactions from the ligrec extra dataset.

interactions.OmniPath()

Request interactions from the omnipath dataset.

interactions.PathwayExtra()

Request interactions from the pathway extra dataset.

interactions.PostTranslational([exclude])

Request all post-translational interactions from [OmniPath] .

interactions.TFmiRNA()

Request interactions from the TF-miRNA dataset.

interactions.TFtarget()

Request interactions from the TF-target dataset.

interactions.Transcriptional()

Request all TF-target interactions from [OmniPath].

interactions.lncRNAmRNA()

Request interactions from the lncRNA-mRNA dataset.

interactions.miRNA()

Request interactions from the miRNA-target dataset.

interactions.import_intercell_network([…])

Import intercellular network combining intercellular annotations and protein interactions.

Other

Constants

constants.InteractionDataset(*args, **kw)

Available interaction datasets in [OmniPath].

constants.License(*args, **kw)

License types.

constants.Organism(*args, **kw)

Organism types.

Options

omnipath.clear_cache()

Remove all cached data from omnipath.options.cache.

omnipath.options

Class defining various omnipath options.