• src
• ..
• 00_Cellranger_QC_plots.Rmd
• 01_saveSCE_splicedUnspliced.R
• 02_splicedUnsplicedQC.R
• 03_splicedUnspliced_scaterQC.R
• 04_Scran_norm.R
• 05_merge_tissues.Rmd
• 06_HCA_sample_QC.Rmd
• 07_red_dim_clust_roughAnnot_cluster_QC_1.Rmd
• 08_Cell_cycle_annotation.Rmd
• 09_Marker_gene_expr_full_dataset.Rmd
• 10_oligos_seurat.Rmd
• 11_oligos_by_tissue.Rmd
• 12_Differential_gene_ex.Rmd
• 13_mix_mod_composition.Rmd
• 15_Trajectory_monocle.R
• 16_Trajectory_slingshot.Rmd
• 19_Test_Dynverse.Rmd
• 20_HCA_gene_ontology.Rmd
• 20_integrate_multiple_ms_datasets.Rmd
• 21_DGE_analysis_sex_age_within_clu.Rmd
• 22_CCA_integration_human.Rmd
• 23_DEG_along_pseudotime.Rmd
• 24_RNA_velocity.Rmd
• 25_pretty_feature_plots.Rmd
• 26_colourblind_friendly_plots.Rmd
• 32_DGE_analysis_tissue_overall_within_clu.Rmd
• 33_cholesterol_biosynthesis_genes.Rmd
• 37_create_plots.Rmd
• 39_microglia.Rmd
• 40_astrocytes.Rmd
• 41_neurons.Rmd
• 42_vascular_cells.Rmd
• 43_HOX_genes.Rmd
• 44_add_fine_clusters_complete_ds.Rmd
• 44_composition_Milo.Rmd
• 44a_composition_Milo_oligos_only.Rmd
• 44b_composition_Milo_astrocytes_only.Rmd
• 44c_composition_Milo_microglia_only.Rmd
• 45_majour_dotplot.Rmd
• 49_all_ct_DGE_analysis_sex_age_within_clu.Rmd
• 50_GO_age_sex_tissue.Rmd
• 50_a_GO_region_OPC.Rmd
• 50_b_GO_region_oligodendrocytes.Rmd
• 51_opcs.Rmd
• 53_shiny.Rmd
• 57_mouse_integration_3_ds.Rmd
• 58_Validation_PDGFRA_PAX3.Rmd
• 63_comparative_QC.Rmd
• 66_Validation_SPARC_RBFOX1_OLIG2.Rmd
• 68_Validation_Nell1_PDGFRA.Rmd
• 69_Validation_HCN2_Olig2_Basescope_dupl.Rmd
• 70_Validation_RBFOX1_FMN1_OLIG2_IF.Rmd
• 71_Validation_RBFOX1_FMN1_OLIG2_IF_manual_quantification.Rmd
• 72_Validation_SPARC_HCN2_OLIG2_IF_FOV_thresholds.Rmd
• 73_Validation_GPNMB_P16P21_IBA1_IF_FOV_thresholds.Rmd
• 74_Validation_RBFOX1_OPALIN_OLIG2_IF_FOV_thresholds.Rmd
• 76_SPARC_OPALIN_OLIG2.Rmd
• 77_summarise_validation.Rmd
• 79_exp_detected_comp.Rmd
• 80_sex_differences_glia_venn.Rmd
• 81_age_differences_glia_venn.Rmd
• 82_Tissue_spec_ageing.Rmd
• 83_validation_RNAscope_PDGFRA_RBFOX1.R