v0.3.0

What's Changed

• Update to v0.3.0 by @earmingol in #2

Full Changelog: v0.2.3...v0.3.0

Summary

Main change includes the implementation of a one-command pipeline to run scCellFie analysis (located in sccellfie.sccellfie_pipeline.run_sccellfie_pipeline().

Other changes are harmonization of docstrings, minor bug fixes and changes in default parameters of a few functions.

v0.2.3

What's Changed

• Update to v0.2.3 by @earmingol in #1

New Contributors

• @earmingol made their first contribution in #1

Full Changelog: v0.2.2...v0.2.3

Commits included

@earmingol
Functions to manipulate GPR rules
cdc71f3
@earmingol
DB - Removed indexes added after including new tasks
cc91de9
@earmingol
Fixed bug when using X that is not a sparse array
988080a
@earmingol
Speeded up generation of inputs and moved gpr functions
2cdea2c
@earmingol
Faster generation of inputs, moved gpr functions, and added adata sub…
ccd9285
@earmingol
Fixed bug when using X that is not a sparse array
d485328
@earmingol
Corrected docstrings
fa19ae1
@earmingol
Added stratified subsampling of adatas
6c5d11f
@earmingol
Added differential analysis
f636e2f
@earmingol
Added functions to explore/modify tasks DB
8cd4b34
@earmingol
Minor modifications to work with new functions
29e8e83
@earmingol
v0.2.3
0cc9e7a
@earmingol
Added stratified subsampling of adata
255550d
@earmingol
Improved docstring about alpha
c0c92c2
@earmingol
Added volcano plot
59ec650
@earmingol
Added normalization function based on total counts
54b0158
@earmingol
Moved differential analysis plots to differential_results.py
d78f1e2
@earmingol
Added plotting to imports
a7af9ad
@earmingol
Removed output of dataframe to generate fig
e5b2440
@earmingol
Removed output of dataframe to generate fig
62b047c
@earmingol
Renamed x_label and y_label to xlabel and ylabel
b5e8399
@earmingol
Added genes to correct in mouse
8e64309
@earmingol
Mouse metabolic genes
acae707
@earmingol
Added new pathways for hormones
11d8dcf
@earmingol
Added/Changed gene nomenclatures
c15b111
@earmingol
Newer versions
6d6d58d
@earmingol
Added mouse genes to correct
c9d6cb7
@earmingol
Added precomputed thresholds for mouse
0841045
@earmingol
Added functions to transform gene names from ensembl to symbol
71aa925
@earmingol
Added imports of missing functions
8df8ce9
@earmingol
Added grid of violin plots
51f11dc

v0.2.2

Full Changelog: v0.2.1...v0.2.2

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

v0.2.1

Full Changelog: v0.2.0...v0.2.1

v0.2.1 - Quick fix for filtering of tasks

v0.2.0

Full Changelog: 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

v0.1.14

Full Changelog: 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.

v0.1.13

Full Changelog: 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

v0.1.12

Full Changelog: 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.

v0.1.11

Full Changelog: v0.1.10...v0.1.11

New features:

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

v.0.1.10

Full Changelog: 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