v0.5.0

What's Changed

• Updating branch by @earmingol in #21
• Updates for v0.5.0 by @earmingol in #22

• Added the option of use layers for TF-IDF analysis
• Included function to generate 3D tensor for tensor decomposition analysis (sccellfie.external.tensor.py)
• Fixed minor bugs for tests.

Full Changelog: v0.4.8...v0.5.0

v0.4.8

What's Changed

• v0.4.8 - Optimized and fixed bugs by @earmingol in #19

Implemented fixes for:

• Pygam not supporting newer versions of scipy (array.A got deprecated).
• Fixed q-value calculation in TF-IDF
• Optimized expression aggregation functions

Plus implementations of memory-efficient optimizations in previous versions:

• Normalization functions of raw counts in AnnData object (v.0.4.6)
• Expression smoothing function (v.0.4.7).

Full Changelog: v0.4.7...v0.4.8

v0.4.7

What's Changed

• Implemented memory efficient smoothing by @earmingol in #18

This includes a memory-efficient implementations of normalization of raw counts in AnnData object (v.0.4.6) and smoothing expression (v.0.4.7).

Full Changelog: v0.4.6...v0.4.7

v0.4.6

What's Changed

• Implemented memory efficient normalization by @earmingol in #17

This includes a memory-efficient normalization of raw counts in AnnData object.

Full Changelog: v0.4.5...v0.4.6

v0.4.5

What's Changed

• v0.4.5 by @earmingol in #15

This includes fixing a bug when converting Ensembl IDs into gene symbols.

Full Changelog: v0.4.4...v0.4.5

v0.4.4

What's Changed

• Updates for readthedocs by @earmingol in #12
• Readthedocs by @earmingol in #13
• Changed "folder" to "output_directory" by @earmingol in #14

Full Changelog: v0.4.3...v0.4.4

v0.4.3

What's Changed

• DB update - Phenylalanine pathways by @earmingol in #8
• v0.4.3 by @earmingol in #9
• This PR includes the following changes:
  - Optimization to the sccellfie.preprocessing.adata_utils.stratified_subsample_adata() function.
  - Update to docstrings
  - Modified saving of CCC network plot (sccellfie.plotting.communication.plot_communication_network()).
  - Implemented functions to export results for scCellFie Metabolic Task Visualizer (see sccellfie.reports.summary)
  - Implemented radial plots (sccellfie.plotting.radial_plot.create_radial_plot())
  - Updated requirements in setup.py

Full Changelog: v0.4.2...v0.4.3

v0.4.2

What's Changed

• v0.4.2 by @earmingol in #6
  • This PR includes a series of improvements:
    • Network plot for visualizing cell-cell communication
    • Added function to select markers from TF-IDF results
    • Harmonized outputs across differential analyses
    • Implemented subsampling in differential analysis
    • Added beeswarm plot for visualizing results from differential analysis
    • Added information about cell fraction using determinant genes of metabolic reactions
    • Added tight_layout parameter to select whether using it or not in plots
    • Improved a few docstrings
    • Fixed minor bugs

EDIT

Phenylalanine-associated tasks were rolled back by @earmingol in #8 and modified as follows:

Changes in #7 were incorrect.

Phenylalanine to phenylacetyl-L-glutaminate only had reactions ALDD19xr (r0545), PHYCBOXL, and PEAMNO since there are no GPR rules for PACCOAL and PHACCOAGLNAC.

For this reason, Phenylalanine to phenylacetyl-L-glutaminate was renamed to Phenylalanine to phenylacetate (via phenylacetaldehyde)

These changes to phenylalanine tasks are not contained in this release source code, containing #7 instead. For lastest version check the main branch

Full Changelog: v0.4.1...v0.4.2

v0.4.1

What's Changed

• v0.4.1 by @earmingol in #4

• Quick fix for using full name imports (sccellfie.plotting instead of sccellfie.pl, and sccellfie.stats instead of sccellfie.tl)
• Update to readme

Full Changelog: v0.4.0...v0.4.1

v0.4.0

scCellFIe v0.4.0

This version includes major changes that substantially improve scCellFie:

• Improved plots, their aesthetics, and labelling.
• Included new preprocessing for both matrices and AnnData objects.
• Completed docstrings for missing functions.
• Added communication module with special analyses for single-cell and spatial data.
• Included pattern analysis using Generalized Additive Models (GAM module).
• Added pseudo-bulks generation of cell types or other groups.
• Improve tests in general.

What's Changed

• v0.4.0 by @earmingol in #3

Full Changelog: v0.3.0...v0.4.0