├── .gitignore ├── Figures ├── Ext_Data_Fig_1 │ ├── bar_layer_plots_simple.R │ └── cre_per_cluster_bar_plots.R ├── Ext_Data_Fig_10 │ ├── 2018-05-25_markers.txt │ ├── cluster_violin_plot.R │ └── layer_and_violin_functions.R ├── Ext_Data_Fig_11 │ └── v1_alm_cross_mapping_cor.R ├── Ext_Data_Fig_12 │ ├── 20171030_inj_qc.tsv │ ├── alm_retrograde_inj_dotplots_actual_targets_dendrogram.R │ ├── prune_leaf_custom.R │ └── visp_retrograde_inj_dotplots_actual_targets_dendrogram.R ├── Ext_Data_Fig_15 │ ├── huang_comparison_figure.R │ ├── huang_dendrogram.R │ ├── linnarsson_comparison.R │ ├── linnarsson_stats.R │ ├── prune_leaf_custom.R │ ├── sankey_functions.R │ ├── tolias_comparison_figure.R │ └── tolias_dendrogram.R ├── Ext_Data_Fig_16 │ ├── cluster_bar_plot.R │ ├── cluster_violin_plot.R │ ├── coexpression_bar_plots.R │ ├── coexpression_functions.R │ ├── layer_and_violin_functions.R │ ├── marker_violins.R │ ├── river_plots.R │ └── sankey_functions.R ├── Ext_Data_Fig_18 │ ├── cluster_violin_plot.R │ ├── coexpression_functions.R │ ├── color_functions.R │ ├── layer_and_violin_functions.R │ ├── prune_leaf_custom.R │ ├── tsne_plots.R │ └── unified_layer_distributions_and_markers.R ├── Ext_Data_Fig_2 │ └── violin_plots.R ├── Ext_Data_Fig_20 │ └── dend_plots.R ├── Ext_Data_Fig_3 │ ├── all_cell_tsne_plot.R │ ├── coclustering_heatmaps_sparse_matrix.R │ ├── pairwise_cluster_heatmaps.R │ └── qc_jitter_plots.R ├── Ext_Data_Fig_4 │ ├── intermediate_fraction_plot.R │ └── qc_jitter_plots.R ├── Ext_Data_Fig_5 │ └── all_markers_heatmap.R ├── Ext_Data_Fig_6 │ ├── cluster_marker_heatmaps.R │ └── markers.csv ├── Ext_Data_Fig_7 │ ├── comparison_figure.R │ └── sankey_functions.R ├── Ext_Data_Fig_8 │ └── saturation_plot.R ├── Ext_Data_Fig_9 │ └── build_dotplot.R ├── Figure_1 │ └── dendrogram_panel.R ├── Figure_2 │ ├── class_comparison_colors_simplified.csv │ ├── color_functions.R │ ├── degenes_alm_visp_barplot.R │ ├── pairwise_DEGene_panels.R │ ├── region_marker_genes_panel.R │ └── tsne_panels.R ├── Figure_3 │ ├── alm_retrograde_inj_dotplot_categories.R │ ├── inj_qc.tsv │ ├── prune_leaf_custom.R │ └── visp_retrograde_inj_dotplot_categories.R ├── Figure_4 │ ├── color_functions.R │ ├── layer_and_violin_functions.R │ ├── prune_leaf_custom.R │ └── unified_layer_distributions_and_markers.R ├── Figure_5 │ ├── color_functions.R │ ├── layer_and_violin_functions.R │ ├── prune_leaf_custom.R │ └── unified_layer_distributions_and_markers.R └── Figure_6 │ ├── L4 IT VISp Rspo1 L5 IT VISp Batf3.rda │ ├── L4 IT VISp Rspo1 L5 IT VISp Hsd11b1 Endou.rda │ ├── L4.2016.dat.rda │ ├── L4.dat.rda │ ├── L4.df.rda │ ├── L4.sampled.df.rda │ ├── L4_comparison_plots.R │ ├── comparison_figure.R │ ├── custom_annotate_cat.R │ ├── gradient.df.list.rda │ ├── l4_gradient_heatmap.R │ ├── pairwise_median_lfc.R │ ├── plotting_functions.R │ ├── sankey_functions.R │ ├── sst150_coords.tsv │ ├── sst300_cl_anno.csv │ ├── sst300_coords.tsv │ ├── sst80_cl_anno.csv │ ├── sst80_coords.tsv │ ├── sst_constellation_positions.xlsx │ ├── sst_constellations.R │ └── sst_river_plot.R ├── LICENSE ├── README.md ├── RNA-seq Analysis ├── ALM.ex.analysis.R ├── DEG.R ├── V1_ALM_compare.R ├── VISp.ex.analysis.R ├── all.cell.markers.heatmap.R ├── annotate.cluster.R ├── annotate.markers.R ├── cl.transition.R ├── cluster.R ├── cluster_hetero.R ├── co_cluster.R ├── compare_1679.R ├── compare_Hrvatin.R ├── compare_JoshWang.R ├── compare_Linnarsson.R ├── compare_Tolias.R ├── consensus.clust.R ├── copy_bam.R ├── fast_tsne.R ├── gradient.R ├── init.R ├── intron.exon.ratio.R ├── markers.R ├── retrograde.R ├── saturation_test.R ├── subsample.all.R ├── subsample.reads.R └── tune_parameter.R └── tasic2018analysis.Rproj /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/.gitignore -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_1/bar_layer_plots_simple.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_1/bar_layer_plots_simple.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_1/cre_per_cluster_bar_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_1/cre_per_cluster_bar_plots.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_10/2018-05-25_markers.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_10/2018-05-25_markers.txt -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_10/cluster_violin_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_10/cluster_violin_plot.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_10/layer_and_violin_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_10/layer_and_violin_functions.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_11/v1_alm_cross_mapping_cor.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_11/v1_alm_cross_mapping_cor.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_12/20171030_inj_qc.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_12/20171030_inj_qc.tsv -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_12/alm_retrograde_inj_dotplots_actual_targets_dendrogram.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_12/alm_retrograde_inj_dotplots_actual_targets_dendrogram.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_12/prune_leaf_custom.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_12/prune_leaf_custom.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_12/visp_retrograde_inj_dotplots_actual_targets_dendrogram.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_12/visp_retrograde_inj_dotplots_actual_targets_dendrogram.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_15/huang_comparison_figure.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_15/huang_comparison_figure.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_15/huang_dendrogram.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_15/huang_dendrogram.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_15/linnarsson_comparison.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_15/linnarsson_comparison.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_15/linnarsson_stats.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_15/linnarsson_stats.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_15/prune_leaf_custom.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_15/prune_leaf_custom.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_15/sankey_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_15/sankey_functions.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_15/tolias_comparison_figure.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_15/tolias_comparison_figure.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_15/tolias_dendrogram.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_15/tolias_dendrogram.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_16/cluster_bar_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_16/cluster_bar_plot.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_16/cluster_violin_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_16/cluster_violin_plot.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_16/coexpression_bar_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_16/coexpression_bar_plots.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_16/coexpression_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_16/coexpression_functions.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_16/layer_and_violin_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_16/layer_and_violin_functions.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_16/marker_violins.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_16/marker_violins.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_16/river_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_16/river_plots.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_16/sankey_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_16/sankey_functions.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_18/cluster_violin_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_18/cluster_violin_plot.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_18/coexpression_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_18/coexpression_functions.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_18/color_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_18/color_functions.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_18/layer_and_violin_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_18/layer_and_violin_functions.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_18/prune_leaf_custom.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_18/prune_leaf_custom.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_18/tsne_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_18/tsne_plots.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_18/unified_layer_distributions_and_markers.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_18/unified_layer_distributions_and_markers.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_2/violin_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_2/violin_plots.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_20/dend_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_20/dend_plots.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_3/all_cell_tsne_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_3/all_cell_tsne_plot.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_3/coclustering_heatmaps_sparse_matrix.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_3/coclustering_heatmaps_sparse_matrix.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_3/pairwise_cluster_heatmaps.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_3/pairwise_cluster_heatmaps.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_3/qc_jitter_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_3/qc_jitter_plots.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_4/intermediate_fraction_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_4/intermediate_fraction_plot.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_4/qc_jitter_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_4/qc_jitter_plots.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_5/all_markers_heatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_5/all_markers_heatmap.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_6/cluster_marker_heatmaps.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_6/cluster_marker_heatmaps.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_6/markers.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_6/markers.csv -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_7/comparison_figure.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_7/comparison_figure.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_7/sankey_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_7/sankey_functions.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_8/saturation_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_8/saturation_plot.R -------------------------------------------------------------------------------- /Figures/Ext_Data_Fig_9/build_dotplot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Ext_Data_Fig_9/build_dotplot.R -------------------------------------------------------------------------------- /Figures/Figure_1/dendrogram_panel.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_1/dendrogram_panel.R -------------------------------------------------------------------------------- /Figures/Figure_2/class_comparison_colors_simplified.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_2/class_comparison_colors_simplified.csv -------------------------------------------------------------------------------- /Figures/Figure_2/color_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_2/color_functions.R -------------------------------------------------------------------------------- /Figures/Figure_2/degenes_alm_visp_barplot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_2/degenes_alm_visp_barplot.R -------------------------------------------------------------------------------- /Figures/Figure_2/pairwise_DEGene_panels.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_2/pairwise_DEGene_panels.R -------------------------------------------------------------------------------- /Figures/Figure_2/region_marker_genes_panel.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_2/region_marker_genes_panel.R -------------------------------------------------------------------------------- /Figures/Figure_2/tsne_panels.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_2/tsne_panels.R -------------------------------------------------------------------------------- /Figures/Figure_3/alm_retrograde_inj_dotplot_categories.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_3/alm_retrograde_inj_dotplot_categories.R -------------------------------------------------------------------------------- /Figures/Figure_3/inj_qc.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_3/inj_qc.tsv -------------------------------------------------------------------------------- /Figures/Figure_3/prune_leaf_custom.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_3/prune_leaf_custom.R -------------------------------------------------------------------------------- /Figures/Figure_3/visp_retrograde_inj_dotplot_categories.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_3/visp_retrograde_inj_dotplot_categories.R -------------------------------------------------------------------------------- /Figures/Figure_4/color_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_4/color_functions.R -------------------------------------------------------------------------------- /Figures/Figure_4/layer_and_violin_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_4/layer_and_violin_functions.R -------------------------------------------------------------------------------- /Figures/Figure_4/prune_leaf_custom.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_4/prune_leaf_custom.R -------------------------------------------------------------------------------- /Figures/Figure_4/unified_layer_distributions_and_markers.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_4/unified_layer_distributions_and_markers.R -------------------------------------------------------------------------------- /Figures/Figure_5/color_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_5/color_functions.R -------------------------------------------------------------------------------- /Figures/Figure_5/layer_and_violin_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_5/layer_and_violin_functions.R -------------------------------------------------------------------------------- /Figures/Figure_5/prune_leaf_custom.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_5/prune_leaf_custom.R -------------------------------------------------------------------------------- /Figures/Figure_5/unified_layer_distributions_and_markers.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_5/unified_layer_distributions_and_markers.R -------------------------------------------------------------------------------- /Figures/Figure_6/L4 IT VISp Rspo1 L5 IT VISp Batf3.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/L4 IT VISp Rspo1 L5 IT VISp Batf3.rda -------------------------------------------------------------------------------- /Figures/Figure_6/L4 IT VISp Rspo1 L5 IT VISp Hsd11b1 Endou.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/L4 IT VISp Rspo1 L5 IT VISp Hsd11b1 Endou.rda -------------------------------------------------------------------------------- /Figures/Figure_6/L4.2016.dat.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/L4.2016.dat.rda -------------------------------------------------------------------------------- /Figures/Figure_6/L4.dat.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/L4.dat.rda -------------------------------------------------------------------------------- /Figures/Figure_6/L4.df.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/L4.df.rda -------------------------------------------------------------------------------- /Figures/Figure_6/L4.sampled.df.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/L4.sampled.df.rda -------------------------------------------------------------------------------- /Figures/Figure_6/L4_comparison_plots.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/L4_comparison_plots.R -------------------------------------------------------------------------------- /Figures/Figure_6/comparison_figure.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/comparison_figure.R -------------------------------------------------------------------------------- /Figures/Figure_6/custom_annotate_cat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/custom_annotate_cat.R -------------------------------------------------------------------------------- /Figures/Figure_6/gradient.df.list.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/gradient.df.list.rda -------------------------------------------------------------------------------- /Figures/Figure_6/l4_gradient_heatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/l4_gradient_heatmap.R -------------------------------------------------------------------------------- /Figures/Figure_6/pairwise_median_lfc.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/pairwise_median_lfc.R -------------------------------------------------------------------------------- /Figures/Figure_6/plotting_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/plotting_functions.R -------------------------------------------------------------------------------- /Figures/Figure_6/sankey_functions.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/sankey_functions.R -------------------------------------------------------------------------------- /Figures/Figure_6/sst150_coords.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/sst150_coords.tsv -------------------------------------------------------------------------------- /Figures/Figure_6/sst300_cl_anno.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/sst300_cl_anno.csv -------------------------------------------------------------------------------- /Figures/Figure_6/sst300_coords.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/sst300_coords.tsv -------------------------------------------------------------------------------- /Figures/Figure_6/sst80_cl_anno.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/sst80_cl_anno.csv -------------------------------------------------------------------------------- /Figures/Figure_6/sst80_coords.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/sst80_coords.tsv -------------------------------------------------------------------------------- /Figures/Figure_6/sst_constellation_positions.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/sst_constellation_positions.xlsx -------------------------------------------------------------------------------- /Figures/Figure_6/sst_constellations.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/sst_constellations.R -------------------------------------------------------------------------------- /Figures/Figure_6/sst_river_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/Figures/Figure_6/sst_river_plot.R -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/README.md -------------------------------------------------------------------------------- /RNA-seq Analysis/ALM.ex.analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/ALM.ex.analysis.R -------------------------------------------------------------------------------- /RNA-seq Analysis/DEG.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/DEG.R -------------------------------------------------------------------------------- /RNA-seq Analysis/V1_ALM_compare.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/V1_ALM_compare.R -------------------------------------------------------------------------------- /RNA-seq Analysis/VISp.ex.analysis.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/VISp.ex.analysis.R -------------------------------------------------------------------------------- /RNA-seq Analysis/all.cell.markers.heatmap.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/all.cell.markers.heatmap.R -------------------------------------------------------------------------------- /RNA-seq Analysis/annotate.cluster.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/annotate.cluster.R -------------------------------------------------------------------------------- /RNA-seq Analysis/annotate.markers.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/annotate.markers.R -------------------------------------------------------------------------------- /RNA-seq Analysis/cl.transition.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/cl.transition.R -------------------------------------------------------------------------------- /RNA-seq Analysis/cluster.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/cluster.R -------------------------------------------------------------------------------- /RNA-seq Analysis/cluster_hetero.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/cluster_hetero.R -------------------------------------------------------------------------------- /RNA-seq Analysis/co_cluster.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/co_cluster.R -------------------------------------------------------------------------------- /RNA-seq Analysis/compare_1679.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/compare_1679.R -------------------------------------------------------------------------------- /RNA-seq Analysis/compare_Hrvatin.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/compare_Hrvatin.R -------------------------------------------------------------------------------- /RNA-seq Analysis/compare_JoshWang.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/compare_JoshWang.R -------------------------------------------------------------------------------- /RNA-seq Analysis/compare_Linnarsson.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/compare_Linnarsson.R -------------------------------------------------------------------------------- /RNA-seq Analysis/compare_Tolias.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/compare_Tolias.R -------------------------------------------------------------------------------- /RNA-seq Analysis/consensus.clust.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/consensus.clust.R -------------------------------------------------------------------------------- /RNA-seq Analysis/copy_bam.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/copy_bam.R -------------------------------------------------------------------------------- /RNA-seq Analysis/fast_tsne.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/fast_tsne.R -------------------------------------------------------------------------------- /RNA-seq Analysis/gradient.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/gradient.R -------------------------------------------------------------------------------- /RNA-seq Analysis/init.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/init.R -------------------------------------------------------------------------------- /RNA-seq Analysis/intron.exon.ratio.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/intron.exon.ratio.R -------------------------------------------------------------------------------- /RNA-seq Analysis/markers.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/markers.R -------------------------------------------------------------------------------- /RNA-seq Analysis/retrograde.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/retrograde.R -------------------------------------------------------------------------------- /RNA-seq Analysis/saturation_test.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/saturation_test.R -------------------------------------------------------------------------------- /RNA-seq Analysis/subsample.all.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/subsample.all.R -------------------------------------------------------------------------------- /RNA-seq Analysis/subsample.reads.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/subsample.reads.R -------------------------------------------------------------------------------- /RNA-seq Analysis/tune_parameter.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/RNA-seq Analysis/tune_parameter.R -------------------------------------------------------------------------------- /tasic2018analysis.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/AllenInstitute/tasic2018analysis/HEAD/tasic2018analysis.Rproj --------------------------------------------------------------------------------