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Flexible pseudobulk designs, robust annotations and improved visualization - #15

Merged

Sergio-ote merged 42 commits into

mainfrom

dev

Oct 7, 2026

Merged

Flexible pseudobulk designs, robust annotations and improved visualization#15
Sergio-ote merged 42 commits into
mainfrom
dev

Commits on Aug 26, 2026
- Add geojson processing rule and script
  NazimMechkouri
  committed
  d68d39f
Commits on Aug 28, 2026
- Apply snakefmt formatting and fix trailing newline
  NazimMechkouri
  committed
  5fffd7e
- Fix: add missing _find_geojson helper in common.smk
  NazimMechkouri
  committed
  ca894d8
Commits on Sep 1, 2026
- Add pseudobulk aggregate and DE rules
  NazimMechkouri
  committed
  1600a1b
Commits on Sep 4, 2026
- Fix concatenation of AnnData objects with sample_batch
  Sergio-ote
  authored
  3d23c59
Commits on Sep 8, 2026
Commits on Sep 9, 2026
- fix: external metadata loading and geojson DAG
  Sergio-ote
  committed
  2f322e1
- Merge pull request #8 from cbib/rule_improvement
  Sergio-ote
  authored
  48f5e90
- refactor: make config paths relative to a base_path
  dgruano
  authored
  aee76d7
- config: modify default profile to run under .test
  dgruano
  authored
  f857909
- fix: make config paths portable and correct workflow defaults
  dgruano
  authored
  e04629c
- fix: add graphviz as dependency to development environment
  dgruano
  committed
  cbeeb51
- Merge pull request #7 from cbib/style/linting-bug
  dgruano
  authored
  61ed844
- feat: support flexible pseudobulk experimental designs
  
  Sergio-ote
  authored and
  dgruano
  committed
  fc42b6a
- docs: document pseudobulk experimental designs
  
  Sergio-ote
  authored and
  dgruano
  committed
  8151228
- fix: missing dependency in the dev environment
  
  Sergio-ote
  authored and
  dgruano
  committed
  f3e9223
- fix: improved pseudobulk formatting and linting
  
  Sergio-ote
  authored and
  dgruano
  committed
  ac214bd
- feature: add customizable UMAP and spatial plot point size directly from config file
  
  Sergio-ote
  authored and
  dgruano
  committed
  afd1cce
- fix: handle annotation availability and external labels, reporting only available cell annotations
  Sergio-ote
  committed
  c87e91b
- fix: relocate legends in UMAP and spatial plots to avoid overlapping issues
  Sergio-ote
  committed
  3094a4d
- fix: clustree and silhouette display
  Sergio-ote
  committed
  f61c6c7
- feat: improve pseudobulk, annotation handling, and plotting
  Sergio-ote
  authored
  9bf65a7
Commits on Sep 11, 2026
- fix: niche overclustering and clustering speed in expensive processing steps
  Sergio-ote
  committed
  33a380e
Commits on Sep 12, 2026
- WIP: overengineered solution using workdir in config
  dgruano
  committed
  934f31e
- fix: reset WIP changes, remove 'directory' from profiles
  dgruano
  committed
  dce31ff
- fix: update test output path on .gitignore
  dgruano
  committed
  5077bd0
- refactor: make default config files templates
  dgruano
  committed
  7d54030
- cleanup: remove zarr_dir param
  dgruano
  committed
  a2cccda
- refactor: set .test directory config as default config
  dgruano
  committed
  9737937
Commits on Sep 15, 2026
Commits on Sep 21, 2026
- fix: require at least three groups for pseudobulk LRT
  Sergio-ote
  committed
  6499c2b
- feat: include one-vs-rest pseudobulk contrasts for multilevel designs
  Sergio-ote
  committed
  d294394
Commits on Sep 23, 2026
- feat(pseudobulk): add DE one-vs-rest and add explicit support for repeated unpaired DE designs
  Sergio-ote
  committed
  04e5a88
Commits on Sep 24, 2026
- fix: prioritize external annotation when provided, add pseudobulk safeguard skip
  Sergio-ote
  committed
  4c061d9
Commits on Oct 7, 2026

Commits

Commits on Aug 26, 2026

Commits on Aug 28, 2026

Commits on Sep 1, 2026

Commits on Sep 4, 2026

Commits on Sep 8, 2026

Commits on Sep 9, 2026

Commits on Sep 11, 2026

Commits on Sep 12, 2026

Commits on Sep 15, 2026

Commits on Sep 21, 2026

Commits on Sep 23, 2026

Commits on Sep 24, 2026

Commits on Oct 7, 2026