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:

  1. Single gene knockdown/knockout

  2. Drug

  3. 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.

Parameters
  • path (Union[str, Path]) – The path to a JSON file containing records for the CREEDS data

  • entity_type (str) – Either ‘gene’, ‘disease’, or ‘chemical’ to specify which dataset to get.

Return type

CREEDSProcessor

Returns

A processor with pre-extracted statements.

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.

statements: List[Statement]

The processed statements (after extract_statements() is run)

class indra.sources.creeds.processor.CREEDSDiseaseProcessor(records)[source]

A processor for disease perturbation experiments in CREEDS.

statements: List[Statement]

The processed statements (after extract_statements() is run)

class indra.sources.creeds.processor.CREEDSGeneProcessor(records)[source]

A processor for single gene perturbation experiments in CREEDS.

statements: List[Statement]

The processed statements (after extract_statements() is run)