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Release 0.1.1 - #3

Merged

jaydu1 merged 16 commits into

mainfrom

release-0.1.1

Sep 30, 2026

Merged

Release 0.1.1#3
jaydu1 merged 16 commits into
mainfrom
release-0.1.1

Commits on Sep 25, 2026
- Stop filtering LFC tests on the mean difference; release 0.1.1
  jaydu1
  committed
  dc4d3f8
- Replogle: fit scripts write the nuisances; remove a local folder
  
  jaydu1
  and
  claude
  committed
  0f09567
Commits on Sep 26, 2026
- Compute size factors from well-expressed genes
  jaydu1
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  1326587
- Add select_propensity_factors; use it for Replogle and Perturb-seq
  
  jaydu1
  and
  claude
  committed
  69f4bb6
Commits on Sep 29, 2026
- Honour fit_gcate offset arrays
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  57f9bbb
- Restore Welch usevar='unequal'
  
  jaydu1
  and
  claude
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  29993a6
- Replogle: drop the legacy log-normalised rank table
  
  jaydu1
  and
  claude
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  2a086fb
- Replogle README: the nuisance file is optional for the notebook
  
  jaydu1
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  345e4ff
- Perturb-seq: align the R tutorial with Python
  
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  claude
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  42dce1c
- Explain library size in the propensity model as a judgement call
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  c0f9762
- Require crispyx >= 0.1.6
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  247db36
Commits on Sep 30, 2026
- Warn when causarray runs under Rosetta on Apple Silicon
  jaydu1
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  9cddc1a
- Rebuild the R environment natively; re-knit the Perturb-seq R tutorial
  
  jaydu1
  and
  claude
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  7551215
- Add the mouse-brain Perturb-seq tutorial; ignore local SEA-AD data
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  2165e50
- Fix review findings in size factors and propensity selection
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  861c228
- Re-run the SEA-AD, Perturb-seq and Replogle tutorials with 0.1.1
  
  jaydu1
  and
  claude
  committed
  c8ce044

Commits

Commits on Sep 25, 2026

Commits on Sep 26, 2026

Commits on Sep 29, 2026

Commits on Sep 30, 2026