v4.0.1 - minor fixes

What's Changed

• Fix internal/external validation when no categorical metadata by @martin5555555555 in #99

New Contributors

• @martin5555555555 made their first contribution in #99

Full Changelog: v4.0.0...v4.0.1

v4.0.0 - Best practices and clustification removed

Features

• Removed clustification feature (BREAKING CHANGE)
• Implemented Snakemake best practices
  • Added GitHub actions for testing and pinning conda environments
  • Containerized the workflow
  • Added JSON schema for configuration and annotation validation

Fixes

• Fixed a bug where UMAP was used but not imported

Documentation

• Added Andreas Hofer (@hoferand) as a co-author
• Added new publication

What's Changed

• Fix bug: umap not imported but used by @bednarsky in #74
• Apply best practices by @hoferand in #76
• Add formatting env and script by @hoferand in #79
• Remove clustification feature by @hoferand in #80
• Add JSON schema by @hoferand in #81
• Don't run GitHub action on every push by @hoferand in #82
• Allow empty lists in config by @hoferand in #83
• Run lint action only when triggered manually by @hoferand in #84
• Add GitHub test action by @hoferand in #85
• Containerize workflow by @hoferand in #86
• Update test by @hoferand in #87
• Pin conda envs by @hoferand in #88
• Add GH action for pinning conda envs by @hoferand in #89
• Fix Conda env pinning action by @hoferand in #90
• Only pin Conda envs for linux-64 by @hoferand in #91
• Fix PR creation by @hoferand in #92
• Update conda env pins by @github-actions[bot] in #93
• Replace pip packages by @hoferand in #95
• Update conda env pins by @github-actions[bot] in #97

New Contributors

• @hoferand made their first contribution in #76
• @github-actions[bot] made their first contribution in #93

Full Changelog: v3.0.3...v4.0.0

v3.0.3 - Minor fixes

What's Changed

• Update environment to avoid bug #72 by @bednarsky in #73

Full Changelog: v3.0.2...v3.0.3

v3.0.2 - Minor fixes & improvements

What's Changed

• Fix stringi version by @bednarsky in #62
• Avoid heatmap config default causing error by @bednarsky in #63
• Give plot_heatmap always enough colors by @bednarsky in #64
• improve-umap-colors-for-only-positive-values by @bednarsky in #71

New Contributors

• @bednarsky made their first contribution in #62

Full Changelog: v3.0.1...v3.0.2

v3.0.1 - Enable module usage using `github()` directive

• to enable module usage using github() directive
  • comment global.yaml (now requires full snakemake installation, not minimal)
• add nodefaults to all env YAML

Full Changelog: v3.0.0...v3.0.1

v3.0.0 - Snakemake 8 compatible

Breaking change: Requires Snakemake >= v8.

Full Changelog: v2.0.0...v3.0.0

v2.0.0 - Performance improvements

Enhancements and new features

• PCA: To improve performance n_components and svd_solver can be configured.
• Heatmap: performance improvements
  • distance matrix calculation done by pdist from scipy and parallelized for observations and features
  • hierarchical clustering using fastcluster
  • observations can be downsampled using configuration n_observations
  • top features can be selected by variability using configuration n_features

The documentation was updated accordingly.

Bug fixes and other performance improvements are not mentioned.

Full Changelog: v1.1.0...v2.0.0

v1.1.0 - small enhancements and bug fixes

Enhancements and new features

• Additional PCA diagnostics: Visualization of the top 10 loadings per principal component using lollipop plots.
• Internal cluster index calculation optional (very compute intensive).
• Enable plotting of all features using the keyword "ALL".
• Enhance Snakemake report using labels.
• Switch from panels to solo plots.
• Switch to data.table usage for accelerated read/write in R.

The documentation was updated accordingly.

Bug fixes and performance improvements are not mentioned.

Full Changelog: v1.0.1...v1.1.0

v1.0.1 - update author ORCID

Full Changelog: v1.0.0...v1.0.1

v1.0.0 - unsupervised analysis now includes cluster analysis methods

enhancements

• added a config flag for 2D plot coord_fixed() option

new features

• Clustering
  • Leiden algorithm
  • Clustification: an ML-based clustering approach that iteratively merges clusters based on misclassification
• Clustree analysis and visualization
• Cluster Validation
  • External cluster indices are determined by comparing all clustering results with all categorical metadata
  • Internal cluster indices are determined for each clustering and [metadata_of_interest]
  • Multiple-criteria decision-making (MCDM) using TOPSIS for ranking clustering results by internal indices
• Visualization
  • all clustering results as 2D and interactive 2D & 3D plots for all available embedings/projections.
  • external cluster indices as hierarchically clustered heatmaps, aggregated in one panel.
  • internal cluster indices as one heatmap with clusterings and selected metadata sorted by TOPSIS ranking from top to bottom and split cluster indices split by type (cost/benefit functions to be minimized/maximized).

documentation

• add scRNA-seq analysis section to the documentation
• update the documentation accordingly (Software, Methods, Features, Examples)
• update report to include all new feature outputs
• update rulegraph

Bug fixes and performance improvements are not mentioned.

Full Changelog: v0.2.0...v1.0.0