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scripts and notebooks from sanbomics
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RNAseq_method_comparison
RNAseq_method_comparison
integration_comparison
integration_comparison
soupX
soupX
3_min_GSEA_tutorial.Rmd
3_min_GSEA_tutorial.Rmd
AUCell_intro.Rmd
AUCell_intro.Rmd
DE_results.csv
DE_results.csv
GO_in_R.Rmd
GO_in_R.Rmd
GO_in_python.ipynb
GO_in_python.ipynb
GSEA_in_python.ipynb
GSEA_in_python.ipynb
PyDeseq2_DE_tutorial.ipynb
PyDeseq2_DE_tutorial.ipynb
RNA_Velocity_scvelo.ipynb
RNA_Velocity_scvelo.ipynb
Random_forest_single_cell_classification.ipynb
Random_forest_single_cell_classification.ipynb
Scanpy_intro_pp_clustering_markers.ipynb
Scanpy_intro_pp_clustering_markers.ipynb
bitfam_random_forest.ipynb
bitfam_random_forest.ipynb
convert_ensemble_ids.ipynb
convert_ensemble_ids.ipynb
count_table_for_deseq_example.csv
count_table_for_deseq_example.csv
doublet_removal_SOLO_scVI.ipynb
doublet_removal_SOLO_scVI.ipynb
h5ad_to_seurat.ipynb
h5ad_to_seurat.ipynb
high_quality_barplots.ipynb
high_quality_barplots.ipynb
high_quality_lineplots.ipynb
high_quality_lineplots.ipynb
high_quality_volcano_plots.ipynb
high_quality_volcano_plots.ipynb
hypergeometric_enrichment_test_p_value.ipynb
hypergeometric_enrichment_test_p_value.ipynb
monocle3_tutorial.Rmd
monocle3_tutorial.Rmd
pseudobulk_pyDeseq2.ipynb
pseudobulk_pyDeseq2.ipynb
python_sequence_alignment.ipynb
python_sequence_alignment.ipynb
salmon_to_deseq.Rmd
salmon_to_deseq.Rmd
sars.ipynb
sars.ipynb
scATAC_intro_R.Rmd
scATAC_intro_R.Rmd
scATAC_intro_R.nb.html
scATAC_intro_R.nb.html
scVI_tools_introduction.ipynb
scVI_tools_introduction.ipynb
scvi_label_transfer.ipynb
scvi_label_transfer.ipynb
seqs.fasta
seqs.fasta
shifted_transformation.ipynb
shifted_transformation.ipynb
simple_scanpy_integration.ipynb
simple_scanpy_integration.ipynb
single_cell_analysis_complete_class.ipynb
single_cell_analysis_complete_class.ipynb
single_cell_gene_co-expression.ipynb
single_cell_gene_co-expression.ipynb
single_r.Rmd
single_r.Rmd
spatial_seq_intro.ipynb
spatial_seq_intro.ipynb
test_significance_t_u_shapiro.ipynb
test_significance_t_u_shapiro.ipynb
tutorial_complex_Heatmap.Rmd
tutorial_complex_Heatmap.Rmd
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