Files in Platypus

Single-Cell Immune Repertoire and Gene Expression Analysis

NEWS.md README.md R/VDJ_db_load.R R/VDJ_phylogenetic_trees_plot.R R/GEX_volcano.R R/VDJ_circos.R R/VDJ_clonal_expansion.R R/GEX_cluster_membership.R R/VDJ_Vgene_usage_barplot.R R/VDJ_clonal_donut.R R/VDJ_Vgene_usage.R R/GEX_heatmap.R R/VGM_expanded_clones.R R/GEX_DEgenes.R R/VDJ_clonotype.R R/VDJ_public.R R/GEX_cluster_genes.R R/VDJ_logoplot_vector.R R/VDJ_phylogenetic_trees.R R/VDJ_overlap_heatmap.R R/VDJ_dynamics.R R/GEX_proportions_barplot.R R/VDJ_ordination.R R/VDJ_extract_germline_MIXCR.R R/VDJ_assemble_for_PnP.R R/VDJ_variants_per_clone.R R/VDJ_build.R R/GEX_GSEA.R R/VDJ_kmers.R R/VDJ_GEX_matrix.R R/GEX_phenotype.R R/VGM_build.R R/VDJ_antigen_integrate.R R/PlatypusDB_AIRR_to_VGM.R R/VDJ_Vgene_usage_stacked_barplot.R R/VDJ_clonotype_v3_w_enclone.R R/VDJ_GEX_clonotype_clusters_circos.R R/VDJ_alpha_beta_Vgene_circos.R R/VDJ_GEX_stats.R R/VDJ_GEX_overlay_clones.R R/PlatypusDB_load_from_disk.R R/GEX_scatter_coexpression.R R/VDJ_VJ_usage_circos.R R/GEX_pairwise_degs.R R/VDJ_diversity.R R/GEX_lineage_trajectories.R R/GEX_gene_visualization.R R/GEX_dottile_plot.R R/Platypus_data.R R/VDJ_network.R R/GEX_cluster_genes_heatmap.R R/VDJ_abundances.R R/VDJ_expand_aberrants.R R/VDJ_rarefaction.R R/VGM_integrate.R R/VDJ_db_annotate.R R/VDJ_contigs_to_vgm.R R/VDJ_call_enclone.R R/GEX_phenotype_per_clone.R R/VDJ_extract_germline_consensus_ref.R R/PlatypusDB_VGM_to_AIRR.R R/VDJ_clonal_barplot.R R/VGM_expand_featurebarcodes.R R/VDJ_plot_SHM.R R/GEX_coexpression_coefficient.R R/VDJ_get_public.R inst/doc/PlatypusV3_agedCNS.Rmd inst/doc/PlatypusV3_agedCNS.R vignettes/PlatypusV3_agedCNS.Rmd man/GEX_GSEA.Rd man/VDJ_VJ_usage_circos.Rd man/VDJ_call_enclone.Rd man/VDJ_phylogenetic_trees_plot.Rd man/VDJ_germline.Rd man/GEX_cluster_genes.Rd man/VDJ_contigs_to_vgm.Rd man/VDJ_clonotype.Rd man/VGM_expanded_clones.Rd man/VDJ_GEX_stats.Rd man/VDJ_rarefaction.Rd man/GEX_lineage_trajectories.Rd man/VDJ_clonal_barplot.Rd man/small_vgm.Rd man/VDJ_GEX_clonotype_clusters_circos.Rd man/GEX_pairwise_DEGs.Rd man/VDJ_clonal_donut.Rd man/PlatypusDB_load_from_disk.Rd man/VDJ_GEX_matrix.Rd man/VDJ_abundances.Rd man/GEX_cluster_genes_heatmap.Rd man/GEX_heatmap.Rd man/VDJ_logoplot_vector.Rd man/GEX_gene_visualization.Rd man/VDJ_expand_aberrants.Rd man/VDJ_alpha_beta_Vgene_circos.Rd man/VDJ_clonal_expansion.Rd man/VDJ_dynamics.Rd man/VDJ_public.Rd man/GEX_proportions_barplot.Rd man/VDJ_variants_per_clone.Rd man/VDJ_ordination.Rd man/VDJ_assemble_for_PnP.Rd man/PlatypusDB_VGM_to_AIRR.Rd man/VDJ_plot_SHM.Rd man/VDJ_phylogenetic_trees.Rd man/VDJ_build.Rd man/GEX_dottile_plot.Rd man/VDJ_diversity.Rd man/VDJ_network.Rd man/GEX_coexpression_coefficient.Rd man/VGM_integrate.Rd man/GEX_phenotype.Rd man/GEX_scatter_coexpression.Rd man/GEX_phenotype_per_clone.Rd man/VDJ_kmers.Rd man/VDJ_antigen_integrate.Rd man/VDJ_overlap_heatmap.Rd man/GEX_volcano.Rd man/VDJ_Vgene_usage_barplot.Rd man/VDJ_Vgene_usage.Rd man/VDJ_circos.Rd man/VDJ_clonotype_v3_w_enclone.Rd man/VDJ_get_public.Rd man/VDJ_db_annotate.Rd man/small_vdj.Rd man/VDJ_GEX_overlay_clones.Rd man/VGM_expand_featurebarcodes.Rd man/GEX_DEgenes.Rd man/VGM_build.Rd man/GEX_cluster_membership.Rd man/VDJ_db_load.Rd man/VDJ_extract_germline_consensus_ref.Rd man/PlatypusDB_AIRR_to_VGM.Rd man/VDJ_Vgene_usage_stacked_barplot.Rd