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updated notebooks #40

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Dec 7, 2023
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updated notebooks #40

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updated notebooks
nathanlazar Dec 5, 2023
45caa7e
black formatting
nathanlazar Dec 5, 2023
818bc4d
update text on plots
nathanlazar Dec 6, 2023
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3 changes: 2 additions & 1 deletion README.md
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Expand Up @@ -19,6 +19,7 @@ Notebooks to reproduce plots from public datasets are included in the `notebooks
- `cpg0016_plots.ipynb` - Create whole-genome plots from cpg0016, calculate Brunner-Munzel statistics and make bar plots.
- `shinyDepMap_benchmark.ipynb` - Load DepMap 19Q3 data and create plots showing an enrichment for within-chromosome arm relationships.
- `DepMap_PB_Driver_Scan_sample.ipynb` - Short sample code for executing the DepMap driver scanning.
- `DepMap_PB_Drivers.ipynb` - Use DepMap 22Q4 data to look at differential proximity bias when TP53 and other genes are wild-type vs loss/gain of function.
- `DepMap_PB_driver_figures.ipynb` - Use DepMap 22Q4 data to look at differential proximity bias when TP53 and other genes are wild-type vs loss/gain of function.
- `DepMap_CNV_analysis` - Look at copy number effects in DepMap data and separate out proximity-bias driven signal.
- `DepMap_version_comparisons.ipynb` - Generate whole-genome plots and Brunner-Munzel probability plots for DepMap 19Q3, 22Q4 and 23Q2 data.
- `scPerturb_tables_heatmaps.ipynb` - Load scRNASeq datasets from scPerturb, run infercnv, compute chromosomal loss, generate result tables, and plot infercnv heatmaps for cells with specific loss.
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