├── 3_min_GSEA_tutorial.Rmd ├── 5x_doublets ├── a.txt ├── analyze_doublets.ipynb └── doublet_methods.ipynb ├── AUCell_intro.Rmd ├── DE_results.csv ├── GO_in_R.Rmd ├── GO_in_python.ipynb ├── GSEA_in_python.ipynb ├── PyDeseq2_DE_tutorial.ipynb ├── RNA_Velocity_scvelo.ipynb ├── RNAseq_method_comparison ├── GTEX_240_sample_ids.csv ├── NOTES.txt ├── analysis.ipynb ├── increasing_depth.csv.gz ├── make_counts_for_polyester.ipynb └── read_generation.Rmd ├── Random_forest_single_cell_classification.ipynb ├── Scanpy_intro_pp_clustering_markers.ipynb ├── bitfam_random_forest.ipynb ├── celloracle_pseudotime_GRN.ipynb ├── convert_ensemble_ids.ipynb ├── count_table_for_deseq_example.csv ├── doublet_removal_SOLO_scVI.ipynb ├── h5ad_to_seurat.ipynb ├── high_quality_barplots.ipynb ├── high_quality_lineplots.ipynb ├── high_quality_volcano_plots.ipynb ├── hypergeometric_enrichment_test_p_value.ipynb ├── integration_comparison ├── harmony.Rmd ├── readme.txt ├── scanorama.ipynb ├── scvi.ipynb ├── seurat_cca.Rmd └── seurat_rpca.Rmd ├── monocle3_tutorial.Rmd ├── paCMAP_examples.ipynb ├── pseudobulk_pyDeseq2.ipynb ├── python_sequence_alignment.ipynb ├── salmon_to_deseq.Rmd ├── sars.ipynb ├── sc2024 ├── annotation_integration.ipynb ├── bad_mapping.ipynb ├── iterative_preprocessing.ipynb ├── preprocessing.ipynb └── readme.txt ├── scATAC_intro_R.Rmd ├── scATAC_intro_R.nb.html ├── scVI_tools_introduction.ipynb ├── scvi_label_transfer.ipynb ├── seqs.fasta ├── shifted_transformation.ipynb ├── simple_scanpy_integration.ipynb ├── simpleaf_alevin_fry_tutorial.txt ├── single_cell_analysis_complete_class.ipynb ├── single_cell_gene_co-expression.ipynb ├── single_r.Rmd ├── soupX ├── readme.txt ├── soupX_R_tutorial.Rmd └── soupX_python_test.ipynb ├── spatial_seq_intro.ipynb ├── test_significance_t_u_shapiro.ipynb └── tutorial_complex_Heatmap.Rmd /3_min_GSEA_tutorial.Rmd: -------------------------------------------------------------------------------- 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