CREEDS (indra.sources.creeds
)
Processor for the CRowd Extracted Expression of Differential Signatures (CREEDS) from [wang2016].
Contains results of differential gene expression experiments extracted from the Gene Expression Omnibus due to three types of perturbations:
Single gene knockdown/knockout
Drug
Disease
- wang2016
Wang, Z., et al. (2016). Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. Nature Communications, **7**(1), 12846.
CREEDS API (indra.sources.creeds.api
)
API for CREEDS.
- indra.sources.creeds.api.process_from_file(path, entity_type)[source]
Process statements from CREEDS in a file.
- indra.sources.creeds.api.process_from_web(entity_type)[source]
Process statements from CREEDS by automatially downloading them.
- Parameters
entity_type (
str
) – Either ‘gene’, ‘disease’, or ‘chemical’ to specify which dataset to get.- Return type
CREEDSProcessor
- Returns
A processor with pre-extracted statements.
CREEDS Processor (indra.sources.creeds.processor
)
Processors for CREEDS data.
- class indra.sources.creeds.processor.CREEDSChemicalProcessor(records)[source]
A processor for chemical perturbation experiments in CREEDS.