Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.2.1...v0.2.2

• Added code to fix gene names when they have alternative names.

Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.2.0...v0.2.1

v0.2.1 - Quick fix for filtering of tasks

Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.14...v0.2.0

Updates

• Added thresholds to keep reactions and tasks based on the genes in AnnData and the reactions kept for each task

Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.13...v0.1.14

New features & updates

• Added new aggregation using mean among top X% values - X defined with top_percent

• Updated metabolic data to include info from Human1 GEM.

Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.12...v0.1.13

New features

• Added option to select what connectivities and distances to used based on label. See sccellfie.expression.smoothing.py

Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.11...v0.1.12

New features:

• Added the option use_raw when running sccellfie.expression.smooth_expression_knn()
• Quick fix for smoothing expression with respect to v0.1.11.

Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.10...v0.1.11

New features:

• Added the option use_raw when running sccellfie.expression.smooth_expression_knn()

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

Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.7...v0.1.8

Commits:

• 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

Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.6...v0.1.7

• Added Trimean as central tendency measure for aggregating expression values (gene expression, reaction activity, metabolic task activity, etc).
• If the reaction activity is 0, the first gene found with that value will be assigned as the determinant gene

Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.5...v0.1.6

• Added small code optimizations to handle GPRs.
• Expanded verbose and progress bar options for handling chunks of data

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.

Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.3...v0.1.4

Fixed minor bug

Implemented functions in sccellfie.spatial

Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.2...v0.1.3

Optimized reaction_activity.py and put placeholder for spatial analyses.

Full Changelog: https://github.com/earmingol/scCellFie/compare/v0.1.1...v0.1.2

Added new functions and testing.

First publication on PYPI