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)[source]

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)[source]

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)[source]

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

Return type:None