scCellFie, inspired by the MATLAB-based CellFie tool, offers advanced analysis of metabolic functions on Python using single-cell and spatial transcriptomics. Efficient and user-friendly, it integrates with Scanpy to extend CellFie's capabilities, enabling in-depth single-cell and spatial metabolic task analysis.
MIT License
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Published by earmingol 3 months ago
Published by earmingol 3 months ago
Published by earmingol 3 months ago
Published by earmingol 6 months ago
Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.12...v0.1.13
Published by earmingol 6 months ago
Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.11...v0.1.12
use_raw
when running sccellfie.expression.smooth_expression_knn()
Published by earmingol 6 months ago
Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.10...v0.1.11
use_raw
when running sccellfie.expression.smooth_expression_knn()
Published by earmingol 6 months ago
Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.8...v0.1.10
Quick fix for improving memory efficiency.
Commits in v0.1.8:
- Added tests for smoothing algorithm
- DALL-E Acknowledgement
- Minor fix to progress bar
- Implemented algorithm for smoothing gene expression based on KNNs
- Uses nanpercentile instead of percentile
- Fixed exclude_zero & added trimean threshold
Published by earmingol 6 months ago
Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.7...v0.1.8
Commits:
Published by earmingol 7 months ago
Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.6...v0.1.7
Published by earmingol 7 months ago
Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.5...v0.1.6
Published by earmingol 8 months ago
Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.4...v0.1.5
Added functions to save and load scCellFie results in AnnData object and fixed minor bugs of manipulating adata.X arrays.
Published by earmingol 9 months ago
Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.3...v0.1.4
Fixed minor bug
Published by earmingol 9 months ago
Implemented functions in sccellfie.spatial
Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.2...v0.1.3
Published by earmingol 9 months ago
Optimized reaction_activity.py and put placeholder for spatial analyses.
Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.1...v0.1.2
Published by earmingol 9 months ago
Added new functions and testing.
Published by earmingol 10 months ago
First publication on PYPI