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4 changes: 2 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -123,7 +123,7 @@ see the tutorial: [![open in Colab](https://colab.research.google.com/assets/col

The PIMMS comparison workflow is a snakemake workflow that runs the all selected PIMMS models and R-models on
a user-provided dataset and compares the results. An example for a publickly available Alzheimer dataset on the
protein groups level is re-built regularly and available at: [rasmussenlab.org/pimms](https://www.rasmussenlab.org/pimms/)
protein groups level is re-built regularly and available at: [rasmussenlab.github.io/pimms](https://rasmussenlab.github.io/pimms/)

It is built on top of
- the [Snakefile_v2.smk](https://github.com/RasmussenLab/pimms/blob/HEAD/project/workflow/Snakefile_v2.smk) (v2 of imputation workflow), specified in on configuration
Expand Down Expand Up @@ -157,7 +157,7 @@ snakemake -s workflow/Snakefile_v2.smk --configfile config/alzheimer_study/confi
snakemake -s workflow/Snakefile_v2.smk --configfile config/alzheimer_study/config.yaml -p -c2 # two cores/process, execute
# after imputation workflow, execute the comparison workflow
snakemake -s workflow/Snakefile_ald_comparison.smk --configfile config/alzheimer_study/comparison.yaml -p -c1
# If you want to build the website locally: https://www.rasmussenlab.org/pimms/
# If you want to build the website locally: https://rasmussenlab.github.io/pimms/
pip install .[docs]
pimms-setup-imputation-comparison -f project/runs/alzheimer_study/
pimms-add-diff-comp -f project/runs/alzheimer_study/ -sf_cp project/runs/alzheimer_study/diff_analysis/AD
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4 changes: 2 additions & 2 deletions project/README.md
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Expand Up @@ -2,7 +2,7 @@
The PIMMS comparison workflow is a snakemake workflow that runs the all selected PIMMS models and R-models on
a user-provided dataset and compares the results. An example for a
[public alzheimer dataset](https://github.com/RasmussenLab/njab/tree/main/docs/tutorial/data)
on the protein groups level is re-built regularly and available at: [rasmussenlab.org/pimms](https://www.rasmussenlab.org/pimms/)
on the protein groups level is re-built regularly and available at: [rasmussenlab.github.io/pimms](https://rasmussenlab.github.io/pimms/)

## Data requirements

Expand Down Expand Up @@ -137,4 +137,4 @@ jupytext --to ipynb -k - -o - 01_1_train_KNN.py | papermill - runs/rev3/01_1_tra
jupytext --to ipynb -k - -o - 01_1_train_KNN_unique_samples.py | papermill - runs/rev3/01_1_train_KNN_unique_samples.ipynb
# new comparison (check if the old nb could be used for this purpose)
jupytext --to ipynb -k - -o - 01_3_revision3.py | papermill - runs/rev3/01_3_revision3.ipynb
```
```
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