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SiSaNA: A Python-based command line interface for Single-Sample Network Analysis

Newman, N. K.; Kuijjer, M. L.; Belova, T.

2025-11-10 bioinformatics
10.1101/2025.11.06.680212 bioRxiv
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MotivationReconstructing and analyzing single-sample regulatory networks has proven useful for understanding mechanisms of regulatory biology and its disruption in disease, but traditionally required a fair amount of programming experience and work from the user. ResultsHere, we present SiSaNA (Single-Sample Network Analysis), a workflow that removes the need of prior programming experience and allows for single-sample regulatory network reconstruction and analysis, all via a command line interface. Using example input files, we walk the user through a tutorial on how to run the SiSaNA pipeline, interpret the results, and obtain high-quality figures summarized in a single HTML file as output. AvailabilitySiSaNA is freely available to install with pip via the Python Package Index. It is additionally available on GitHub at https://github.com/kuijjerlab/sisana. Example input files can be found at https://doi.org/10.5281/zenodo.17190642.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.