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Collection of generic code for analysing single cell data sets

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scArches
scArches
 
 
AddModuleScore_LR.R
AddModuleScore_LR.R
 
 
AddModuleScore_general.R
AddModuleScore_general.R
 
 
Box_plot_from_seurat.R
Box_plot_from_seurat.R
 
 
Cell_dive.R
Cell_dive.R
 
 
Gene_correlation_cell.R
Gene_correlation_cell.R
 
 
Gene_expression_correlation_sample.R
Gene_expression_correlation_sample.R
 
 
Harmony_key_error_workaround.R
Harmony_key_error_workaround.R
 
 
NN_analysis.R
NN_analysis.R
 
 
Pseudobulk_Dseq2.R
Pseudobulk_Dseq2.R
 
 
README.md
README.md
 
 
Ratio_expr_JL_lab.R
Ratio_expr_JL_lab.R
 
 
Reading_in_pre_processing_Seurat.R
Reading_in_pre_processing_Seurat.R
 
 
TF_regulon_plot_from_scMEGA
TF_regulon_plot_from_scMEGA
 
 
Xenium_choose_genes.R
Xenium_choose_genes.R
 
 
add_umap_subclusters_JIA.R
add_umap_subclusters_JIA.R
 
 
bulk_RNA_analysis.R
bulk_RNA_analysis.R
 
 
bulk_seq_Go_terms.R
bulk_seq_Go_terms.R
 
 
check_propotions_of_cells.R
check_propotions_of_cells.R
 
 
cleanup_unix.txt
cleanup_unix.txt
 
 
cluster_tree_heierchy.R
cluster_tree_heierchy.R
 
 
corr_heatmap.R
corr_heatmap.R
 
 
ecotyper_fetch_data.R
ecotyper_fetch_data.R
 
 
find_mouse_orthologues_and_AddModuleScore.R
find_mouse_orthologues_and_AddModuleScore.R
 
 
gene_module_psudobulk.R
gene_module_psudobulk.R
 
 
gsFisher_from_pb.R
gsFisher_from_pb.R
 
 
gsFisher_goTerms.R
gsFisher_goTerms.R
 
 
harmony_basic.R
harmony_basic.R
 
 
heat_map_from_seurat_dotplot.R
heat_map_from_seurat_dotplot.R
 
 
inflam_corr_korsunskeyetal2022.R
inflam_corr_korsunskeyetal2022.R
 
 
monocle2.R
monocle2.R
 
 
pre_process_SoupX_doublet_Seurat.R
pre_process_SoupX_doublet_Seurat.R
 
 
proprtions_cluster.R
proprtions_cluster.R
 
 
pseudobulk_modules_for_all_cell_types.R
pseudobulk_modules_for_all_cell_types.R
 
 
pseudobulk_new.R
pseudobulk_new.R
 
 
rename_Seurat_idents.R
rename_Seurat_idents.R
 
 
sample_tx_corr.R
sample_tx_corr.R
 
 
scProportionTest.R
scProportionTest.R
 
 
volcano_plot.R
volcano_plot.R
 
 
write_out_seurat_obj.R
write_out_seurat_obj.R
 
 

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General_singleCell_code

Collection of generic code for analysing single cell data sets

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Collection of generic code for analysing single cell data sets

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