Skip to content

Add citation and upstream reference for original SPLIT method #1

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
mariiabilous wants to merge 5 commits into
base: main
Choose a base branch
from
Open

Add citation and upstream reference for original SPLIT method #1

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
6d024be
Enhance README with links to SPLIT resources
mariiabilous Jun 18, 2026
08e6605
Add upstream and paper URLs to project metadata
mariiabilous Jun 18, 2026
30c39a7
Update DISCOVERY.md with upstream citation
mariiabilous Jun 18, 2026
66262db
Update SPLIT-ST workflow notebook with citations
mariiabilous Jun 18, 2026
8bfad67
Format citation for SPLIT publication in README
mariiabilous Jun 18, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion DISCOVERY.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,8 @@
- **Description**: Spatial transcript purification for contamination-aware spatial transcriptomics workflows
- **License**: GPL-3
- **Repository**: https://github.com/bdsc-tds/SPLIT

- **Upstream citation**: Bilous et al., *Nature Methods* (2026), https://doi.org/10.1038/s41592-026-03089-8

## Existing py- Mirror Check

- **py-SPLIT exists in omicverse?**: No - this is a new port.
Expand Down
14 changes: 11 additions & 3 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@

# SPLIT-ST

A **pure-Python re-implementation of SPLIT** for spatial transcriptomics purification.
A **pure-Python re-implementation of [SPLIT](https://github.com/bdsc-tds/SPLIT)** for spatial transcriptomics purification.

- AnnData-native — works directly with cell x gene spatial matrices
- No `rpy2`, no R install, no RCTD/Seurat object dependency
Expand Down Expand Up @@ -235,8 +235,16 @@ from splitst import (

## Citation

If you use this package, please cite the original SPLIT work and acknowledge this repository for the Python port.
This package is a Python re-implementation of the original SPLIT method. If you use this package, please cite the original SPLIT publication:

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

Please also acknowledge this repository when using the Python port.

## License

GNU GPLv3 — matching the upstream SPLIT license.
GNU GPLv3 — matching the upstream [SPLIT](https://github.com/bdsc-tds/SPLIT) license.
4 changes: 4 additions & 0 deletions examples/split_workflow.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,10 @@
"# SPLIT-ST workflow\n",
"\n",
"This notebook runs the standalone Python SPLIT workflow on a deterministic AnnData fixture."

Please cite: Bilous et al., **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
]
},
{
Expand Down
2 changes: 2 additions & 0 deletions pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,6 +43,8 @@ dev = [
Homepage = "https://github.com/omicverse/py-SPLIT"
Repository = "https://github.com/omicverse/py-SPLIT"
Issues = "https://github.com/omicverse/py-SPLIT/issues"
Upstream = "https://github.com/bdsc-tds/SPLIT"
Paper = "https://doi.org/10.1038/s41592-026-03089-8"

[tool.setuptools.packages.find]
include = ["splitst*"]
Expand Down