SPIA

An exporter for signaling pathway impact analysis (SPIA) described by [Tarca2009].

Tarca2009

Tarca, A. L., et al (2009). A novel signaling pathway impact analysis. Bioinformatics, 25(1), 75–82.

To run this module on an arbitrary BEL graph, use the command python -m pybel_tools.analysis.spia.

See also

https://bioconductor.org/packages/release/bioc/html/SPIA.html

pybel_tools.analysis.spia.bel_to_spia_matrices(graph)

Create an excel sheet ready to be used in SPIA software.

Parameters

graph (BELGraph) – BELGraph

Return type

Mapping[str, DataFrame]

Returns

dictionary with matrices

pybel_tools.analysis.spia.spia_matrices_to_excel(spia_matrices, path)

Export a SPIA data dictionary into an Excel sheet at the given path.

Note

# The R import should add the values: # [“nodes”] from the columns # [“title”] from the name of the file # [“NumberOfReactions”] set to “0”

Return type

None

pybel_tools.analysis.spia.spia_matrices_to_tsvs(spia_matrices, directory)

Export a SPIA data dictionary into a directory as several TSV documents.

Return type

None