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Add citation and upstream reference for original SPLIT method#1

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mariiabilous wants to merge 5 commits into
omicverse:mainfrom
mariiabilous:patch-1
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Add citation and upstream reference for original SPLIT method#1
mariiabilous wants to merge 5 commits into
omicverse:mainfrom
mariiabilous:patch-1

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Summary

Thank you for developing a pure-Python re-implementation of SPLIT and for making the method more accessible to Python/AnnData users.

This PR adds proper attribution and citation for the original SPLIT method, which this repository re-implements in Python.

The changes add:

  • A direct link to the original SPLIT R package: https://github.com/bdsc-tds/SPLIT
  • The formal citation to the SPLIT publication in Nature Methods
  • Additional citation/linking in repository documentation and metadata where SPLIT is mentioned
  • A clarification that this Python package is independently developed and has not been validated by the original SPLIT authors

Motivation

Since this package is described as a pure-Python re-implementation of SPLIT, the original SPLIT method and publication should be clearly linked and cited in the README and related documentation. This helps users correctly attribute the original method and makes the relationship between py-SPLIT/SPLIT-ST and the upstream SPLIT package explicit.

I am the author of the original SPLIT package, and I appreciate the effort to make the approach available in the Python ecosystem. At the same time, this Python implementation is independently developed and maintained. The original SPLIT authors have not validated this implementation, and we cannot guarantee that it reproduces the results of the original R package or the results reported in the SPLIT publication.

In addition, the original SPLIT R package is under active development and improvement. Therefore, we cannot guarantee that the latest features, updates, or methodological changes from the original SPLIT package are incorporated in this Python re-implementation.

Citation added

Bilous, M., Buszta, D., Bac, J., Kang, S., Dong, Y., Tissot, S., Andre, S., Alexandre-Gaveta, M., Voize, C., Peters, S., Homicsko, K. & Gottardo, R.
Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.
Nature Methods (2026). https://doi.org/10.1038/s41592-026-03089-8

Original SPLIT R package: https://github.com/bdsc-tds/SPLIT

Updated README to include links to the original SPLIT repository and publication.
Added upstream citation for SPLIT R package.
Added citation and references for SPLIT-ST workflow.
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