Files in supatt-lab/SingCellaR

SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data

R/Import.R R/RcppExports.R R/SingleCellClasses.R R/SingleCellGenerics.R R/SingleCellPlots.R R/SingleCellRNASeq.R R/SingleCellUtils.R R/SingleCell_Integration.R R/zzz.R README.md man/Build_AUCell_Rankings.Rd man/Build_AUCell_Rankings_Fast.Rd man/DoubletDetection_with_scrublet.Rd man/Run_AUCell.Rd man/Run_fGSEA_analysis.Rd man/Run_fGSEA_for_a_selected_cluster_vs_the_rest_of_clusters.Rd man/Run_fGSEA_for_multiple_comparisons.Rd man/SingCellaR.Rd man/TargetSeq_filter_cells_and_genes.Rd man/TargetSeq_load_cell_metadata.Rd man/TargetSeq_plot_cells_annotation.Rd man/TargetSeq_process_cells_annotation.Rd man/add_cell_cycle_genes_score.Rd man/clustering_KMeansOnKNN_Graph.Rd man/export_marker_genes_to_table.Rd man/filter_cells_and_genes.Rd man/findMarkerGenes.Rd man/getCellsFromClusters.Rd man/getMarkerGenesInfo.Rd man/get_cells_annotation.Rd man/get_clusters.Rd man/get_dfm.result.Rd man/get_dir_path_10x_matrix.Rd man/get_fa2_graph.layout.Rd man/get_genes_metadata.Rd man/get_gmtGeneSets.Rd man/get_knn_graph.graph.Rd man/get_knn_graph.layout.Rd man/get_lsi.result.Rd man/get_marker_genes.Rd man/get_nnmf.result.Rd man/get_normalized_umi.Rd man/get_pca.result.Rd man/get_regressout_log_data.Rd man/get_sample_uniq_id.Rd man/get_tsne.result.Rd man/get_umap.result.Rd man/get_umi_count.Rd man/get_variable_genes_basic.Rd man/get_variable_genes_by_fitting_GLM_model.Rd man/get_variable_genes_for_integrative_data_by_fitting_GLM_model.Rd man/identifyClusters.Rd man/identifyDifferentialGenes.Rd man/identifyDifferentialGenes_for_all_clusters.Rd man/identifyDifferentialGenes_in_a_cluster_vs_the_rest_of_clusters.Rd man/identifyDifferentialGenes_in_multiple_clusters_vs_the_rest_of_clusters.Rd man/identifyGSEAPrerankedGenes.Rd man/identifyGSEAPrerankedGenes_for_all_clusters.Rd man/identifyGSEAPrerankedGenes_in_a_cluster_vs_the_rest_of_clusters.Rd man/identify_potentially_merging_clusters.Rd man/listAvailableGeneSets.Rd man/load_gene_expression_from_a_file.Rd man/load_matrices_from_cellranger.Rd man/merge_clusters.Rd man/normalize_UMIs.Rd man/plot_3D_knn_graph_label_by_a_signature_gene_set.Rd man/plot_3D_knn_graph_label_by_clusters.Rd man/plot_3D_knn_graph_label_by_gene.Rd man/plot_PCA_Elbowplot.Rd man/plot_ShortestPath_on_3D_knn_graph.Rd man/plot_ShortestPath_on_forceDirectedGraph_label_by_clusters.Rd man/plot_UMIs_of_HouseKeepingGenes.Rd man/plot_UMIs_vs_Detected_genes.Rd man/plot_bubble_for_genes_per_cluster.Rd man/plot_bubble_for_genes_per_custom_group_of_cells.Rd man/plot_cells_annotation.Rd man/plot_diffusionmap_label_by_clusters.Rd man/plot_diffusionmap_label_by_genes.Rd man/plot_diffusionmap_label_by_multiple_gene_sets.Rd man/plot_forceDirectedGraph_label_by_AUCell_score.Rd man/plot_forceDirectedGraph_label_by_a_feature_of_interest.Rd man/plot_forceDirectedGraph_label_by_a_signature_gene_set.Rd man/plot_forceDirectedGraph_label_by_clusters.Rd man/plot_forceDirectedGraph_label_by_genes.Rd man/plot_forceDirectedGraph_label_by_multiple_gene_sets.Rd man/plot_forceDirectedGraph_label_by_multiple_gene_sets_with_limited_sampleID.Rd man/plot_forceDirectedGraph_label_by_qc.Rd man/plot_forceDirectedGraph_label_by_sampleID.Rd man/plot_forceDirectedGraph_label_by_selected_sampleID.Rd man/plot_heatmap_for_differential_genes.Rd man/plot_heatmap_for_fGSEA_all_clusters.Rd man/plot_heatmap_for_marker_genes.Rd man/plot_jaccard_similarity_among_clusters.Rd man/plot_tsne_label_by_AUCell_score.Rd man/plot_tsne_label_by_a_feature_of_interest.Rd man/plot_tsne_label_by_a_signature_gene_set.Rd man/plot_tsne_label_by_clusters.Rd man/plot_tsne_label_by_genes.Rd man/plot_tsne_label_by_multiple_gene_sets.Rd man/plot_tsne_label_by_multiple_gene_sets_with_limited_sampleID.Rd man/plot_tsne_label_by_qc.Rd man/plot_tsne_label_by_sampleID.Rd man/plot_tsne_label_by_selected_sampleID.Rd man/plot_umap_label_by_AUCell_score.Rd man/plot_umap_label_by_a_feature_of_interest.Rd man/plot_umap_label_by_a_signature_gene_set.Rd man/plot_umap_label_by_clusters.Rd man/plot_umap_label_by_genes.Rd man/plot_umap_label_by_multiple_gene_sets.Rd man/plot_umap_label_by_multiple_gene_sets_with_limited_sampleID.Rd man/plot_umap_label_by_qc.Rd man/plot_umap_label_by_sampleID.Rd man/plot_umap_label_by_selected_sampleID.Rd man/plot_variable_genes.Rd man/plot_violin_for_differential_genes.Rd man/plot_violin_for_genes_per_custom_group_of_cells.Rd man/plot_violin_for_marker_genes.Rd man/preprocess_integration.Rd man/preprocess_integration_for_ADT.Rd man/process_cells_annotation.Rd man/remove_clusters.Rd man/remove_unwanted_confounders.Rd man/remove_unwanted_genes_from_variable_gene_set.Rd man/runCombat.Rd man/runDiffusionMap.Rd man/runFA2_ForceDirectedGraph.Rd man/runHarmony.Rd man/runKBET.Rd man/runKNN_Graph.Rd man/runLISI.Rd man/runLiger_online_iNMF.Rd man/runNNMF.Rd man/runPCA.Rd man/runScanorama.Rd man/runSeuratIntegration.Rd man/runSeuratIntegration_with_rpca.Rd man/runSupervised_Harmony.Rd man/runTSNE.Rd man/runUMAP.Rd man/show-methods.Rd man/sub_clusters.Rd man/subsample_cells.Rd