Add FlashDeconv to ecosystem packages

[cafferychen777]

Checklist for adding packages

Mandatory

Name of the tool: FlashDeconv

Short description: High-performance spatial transcriptomics deconvolution using structure-preserving randomized sketching. Processes 1M spots in ~3 minutes with linear O(N) scaling.

How does the package use scverse data structures: FlashDeconv provides a scanpy-compatible API (fd.tl.deconvolve()) that takes AnnData objects as input (spatial data and reference scRNA-seq) and stores cell type proportions directly in adata.obsm['flashdeconv'], adata.obs columns for each cell type, and parameters in adata.uns. This enables seamless integration with scanpy visualization (sc.pl.spatial()) and downstream analysis.

• The code is publicly available under an OSI-approved license (GPL-3.0)
• The package provides versioned releases (v0.1.0, v0.1.1, v0.1.2)
• The package can be installed from a standard registry (PyPI: pip install flashdeconv)
• Automated tests cover essential functions of the package and a reasonable range of inputs and conditions
• Continuous integration (CI) automatically executes these tests on each push or pull request (GitHub Actions)
• The package provides API documentation via a website or README (comprehensive README with API reference)
• The package uses scverse datastructures where appropriate (AnnData for both input and output)
• I am an author or maintainer of the tool and agree on listing the package on the scverse website

Recommended

• Please announce this package on scverse communication channels (zulip, discourse, twitter)

• Please tag the author(s) these announcements. Handles (e.g. @scverse_team) to include are:

  • Twitter: @pollen_yang

• The package provides tutorials (Resolution Horizon tutorial in docs/)

• The package uses the scverse cookiecutter template

Publication

Yang, C., Chen, J. & Zhang, X. FlashDeconv enables atlas-scale, multi-resolution spatial deconvolution via structure-preserving sketching. bioRxiv (2025). https://doi.org/10.64898/2025.12.22.696108

Links

• GitHub: https://github.com/cafferychen777/flashdeconv
• PyPI: https://pypi.org/project/flashdeconv/
• Reproducibility: https://github.com/cafferychen777/flashdeconv-reproducibility