GitHub - mousepixels/sanbomics_scripts: scripts and notebooks from sanbomics

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Name		Name	Last commit message	Last commit date
Latest commit History 60 Commits
RNAseq_method_comparison		RNAseq_method_comparison
integration_comparison		integration_comparison
sc2024		sc2024
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
celloracle_pseudotime_GRN.ipynb		celloracle_pseudotime_GRN.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
paCMAP_examples.ipynb		paCMAP_examples.ipynb
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
simpleaf_alevin_fry_tutorial.txt		simpleaf_alevin_fry_tutorial.txt
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