add-src-08

imsb-uke · Dec 5, 2024 · e0634cb · e0634cb
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diff --git a/notebooks/08_pca_pseudotime/README.md b/notebooks/08_pca_pseudotime/README.md
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+## Processing and sample annotations
+
+Includes scripts to anaylsis principal components (PCs) and perform pseudotime.
+
+1. `pc_ratio.ipynb` and `summarize_PC_contributors.ipynb` includes code to have on overview of variances captured by individual PCs and to find correlation between cell types and PCs
+2. `compute_pseudotime.ipynb`
+3. Folder `ps_per_disease` includes pseudotime done per disease
+
+In the working directly, the .h5ad object will be saved at `xenium_outs/adata_polygon_reduced_pseudotime.h5ad` with pseudotime i column dpt_pseudotime.
diff --git a/notebooks/08_pca_pseudotime/compute_pseudotime.ipynb b/notebooks/08_pca_pseudotime/compute_pseudotime.ipynb
diff --git a/notebooks/08_pca_pseudotime/pc_ratio.ipynb b/notebooks/08_pca_pseudotime/pc_ratio.ipynb
diff --git a/notebooks/08_pca_pseudotime/ps_per_disease/ps_per_disease.ipynb b/notebooks/08_pca_pseudotime/ps_per_disease/ps_per_disease.ipynb
diff --git a/notebooks/08_pca_pseudotime/ps_per_disease/trajectories_per_disease.ipynb b/notebooks/08_pca_pseudotime/ps_per_disease/trajectories_per_disease.ipynb
diff --git a/notebooks/08_pca_pseudotime/summarize_PC_contributors.ipynb b/notebooks/08_pca_pseudotime/summarize_PC_contributors.ipynb
diff --git a/notebooks/08_other/Protein_analysis.ipynb → notebooks/09_other/Protein_analysis.ipynb b/notebooks/08_other/Protein_analysis.ipynb → notebooks/09_other/Protein_analysis.ipynb
diff --git a/notebooks/08_other/plot_glom_pec.ipynb → notebooks/09_other/plot_glom_pec.ipynb b/notebooks/08_other/plot_glom_pec.ipynb → notebooks/09_other/plot_glom_pec.ipynb
diff --git a/...books/08_other/plot_glom_pec_slide2.ipynb → ...books/09_other/plot_glom_pec_slide2.ipynb b/...books/08_other/plot_glom_pec_slide2.ipynb → ...books/09_other/plot_glom_pec_slide2.ipynb