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Update code to latest specification
* Only two-sample liner model (i.e. Student's t-test) * Rank by log fold change difference * Specification of for time simulation dataset * New status.py script * Calculate log normalised counts for the endothelial dataset * Add rankby_abs to scanpy * Add pval.type = "some" to scran Other small changes
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- Snakefile.py 52 additions, 19 deletionsSnakefile.py
- code/method-pars.R 4 additions, 3 deletionscode/method-pars.R
- code/plot-utils.R 2 additions, 4 deletionscode/plot-utils.R
- code/prep-endothelial.R 4 additions, 0 deletionscode/prep-endothelial.R
- code/run-difference.R 27 additions, 35 deletionscode/run-difference.R
- code/run-lm.R 32 additions, 15 deletionscode/run-lm.R
- code/run-random.R 1 addition, 1 deletioncode/run-random.R
- code/run-scanpy.R 2 additions, 1 deletioncode/run-scanpy.R
- code/run-seurat.R 0 additions, 5 deletionscode/run-seurat.R
- code/run-smash.R 2 additions, 82 deletionscode/run-smash.R
- code/simulation-pars.R 4 additions, 3 deletionscode/simulation-pars.R
- config.yaml 2 additions, 1 deletionconfig.yaml
- status.py 56 additions, 10 deletionsstatus.py
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