In getSubnetworkFromIndra(), the arguments paper_count_cutoff, correlation_cutoff, and protein_level_data are deprecated. Supplying any of them gives a warning. They will become defunct in the next Bioconductor release and be removed in the one after.
paper_count_cutoff is now ignored. INDRA does not return paper counts (the paperCount column is always 1), so the default had no effect and values of 2 or more removed every edge and raised an error.
correlation_cutoff and protein_level_data still work during the deprecation period. The paperCount and correlation columns of the returned edges will be removed when the arguments become defunct.
MSstatsBioNet 0.99.0
Added function getSubnetworkFromIndra to extract biomolecular subnetworks from the INDRA database.
Added function visualizeNetworks to visualize networks in Cytoscape desktop.
Added vignette
MSstatsBioNet 0.1.0
Added a NEWS.md file to track changes to the package.