| .onLoad |
Source code
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| Build_AUCell_Rankings |
Man page
Source code
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| Build_AUCell_Rankings_Fast |
Man page
Source code
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| CustomPalette |
Source code
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| DoubletDetection_with_scrublet |
Man page
Source code
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| Run_AUCell |
Man page
Source code
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| Run_fGSEA_analysis |
Man page
Source code
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| Run_fGSEA_for_a_selected_cluster_vs_the_rest_of_clusters |
Man page
Source code
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| Run_fGSEA_for_multiple_comparisons |
Man page
Source code
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| SingCellaR |
Man page
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| SingCellaR-class |
Man page
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| TargetSeq_filter_cells_and_genes |
Man page
Source code
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| TargetSeq_load_cell_metadata |
Man page
Source code
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| TargetSeq_plot_cells_annotation |
Man page
Source code
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| TargetSeq_process_cells_annotation |
Man page
Source code
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| add_cell_cycle_genes_score |
Man page
Source code
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| annoy_search_parallel_cpp |
Source code
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| binarizeMat |
Source code
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| clustering_KMeansOnKNN_Graph |
Man page
Source code
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| compute_weights |
Source code
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| count_divided_by_libsize |
Source code
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| count_expressing_cells |
Source code
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| export_marker_genes_to_table |
Man page
Source code
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| filter_cells_and_genes |
Man page
Source code
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| findMarkerGenes |
Man page
Source code
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| getCellsFromClusters |
Man page
Source code
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| getDetectedGenesPerCell |
Source code
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| getExpressingCellsPerGene |
Source code
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| getMarkerGenesInfo |
Man page
Source code
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| get_cells_annotation |
Man page
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| get_clusters |
Man page
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| get_dfm.result |
Man page
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| get_dir_path_10x_matrix |
Man page
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| get_fa2_graph.layout |
Man page
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| get_genes_metadata |
Man page
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| get_gmtGeneSets |
Man page
Source code
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| get_knn_graph.graph |
Man page
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| get_knn_graph.layout |
Man page
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| get_lsi.result |
Man page
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| get_marker_genes |
Man page
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| get_nnmf.result |
Man page
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| get_normalized_umi |
Man page
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| get_pca.result |
Man page
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| get_regressout_log_data |
Man page
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| get_sample_uniq_id |
Man page
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| get_tsne.result |
Man page
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| get_umap.result |
Man page
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| get_umi_count |
Man page
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| get_variable_genes_basic |
Man page
Source code
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| get_variable_genes_by_fitting_GLM_model |
Man page
Source code
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| get_variable_genes_for_integrative_data_by_fitting_GLM_model |
Man page
Source code
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| identifyClusters |
Man page
Source code
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| identifyDifferentialGenes |
Man page
Source code
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| identifyDifferentialGenes_for_all_clusters |
Man page
Source code
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| identifyDifferentialGenes_in_a_cluster_vs_the_rest_of_clusters |
Man page
Source code
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| identifyDifferentialGenes_in_multiple_clusters_vs_the_rest_of_cl |
Man page
Source code
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| identifyGSEAPrerankedGenes |
Man page
Source code
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| identifyGSEAPrerankedGenes_for_all_clusters |
Man page
Source code
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| identifyGSEAPrerankedGenes_in_a_cluster_vs_the_rest_of_clusters |
Man page
Source code
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| identifyKNN |
Source code
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| identify_potentially_merging_clusters |
Man page
Source code
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| listAvailableGeneSets |
Man page
Source code
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| load_custom_MEX_matrices |
Source code
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| load_gene_expression_from_a_file |
Man page
Source code
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| load_matrices_from_cellranger |
Man page
Source code
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| makeBinaryMatrix |
Source code
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| makeBinaryMatrix_for_float |
Source code
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| merge_clusters |
Man page
Source code
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| normalize_ADTs |
Source code
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| normalize_UMIs |
Man page
Source code
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| plot_3D_knn_graph_label_by_a_signature_gene_set |
Man page
Source code
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| plot_3D_knn_graph_label_by_clusters |
Man page
Source code
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| plot_3D_knn_graph_label_by_gene |
Man page
Source code
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| plot_PCA_Elbowplot |
Man page
Source code
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| plot_ShortestPath_on_3D_knn_graph |
Man page
Source code
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| plot_ShortestPath_on_forceDirectedGraph_label_by_clusters |
Man page
Source code
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| plot_UMIs_of_HouseKeepingGenes |
Man page
Source code
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| plot_UMIs_vs_Detected_genes |
Man page
Source code
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| plot_bubble_for_genes_per_cluster |
Man page
Source code
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| plot_bubble_for_genes_per_custom_group_of_cells |
Man page
Source code
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| plot_cells_annotation |
Man page
Source code
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| plot_diffusionmap_label_by_clusters |
Man page
Source code
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| plot_diffusionmap_label_by_genes |
Man page
Source code
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| plot_diffusionmap_label_by_multiple_gene_sets |
Man page
Source code
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| plot_forceDirectedGraph_label_by_AUCell_score |
Man page
Source code
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| plot_forceDirectedGraph_label_by_a_feature_of_interest |
Man page
Source code
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| plot_forceDirectedGraph_label_by_a_signature_gene_set |
Man page
Source code
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| plot_forceDirectedGraph_label_by_clusters |
Man page
Source code
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| plot_forceDirectedGraph_label_by_genes |
Man page
Source code
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| plot_forceDirectedGraph_label_by_multiple_gene_sets |
Man page
Source code
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| plot_forceDirectedGraph_label_by_multiple_gene_sets_with_limited |
Man page
Source code
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| plot_forceDirectedGraph_label_by_qc |
Man page
Source code
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| plot_forceDirectedGraph_label_by_sampleID |
Man page
Source code
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| plot_forceDirectedGraph_label_by_selected_sampleID |
Man page
Source code
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| plot_heatmap_for_differential_genes |
Man page
Source code
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| plot_heatmap_for_fGSEA_all_clusters |
Man page
Source code
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| plot_heatmap_for_marker_genes |
Man page
Source code
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| plot_jaccard_similarity_among_clusters |
Man page
Source code
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| plot_tsne_label_by_AUCell_score |
Man page
Source code
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| plot_tsne_label_by_a_feature_of_interest |
Man page
Source code
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| plot_tsne_label_by_a_signature_gene_set |
Man page
Source code
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| plot_tsne_label_by_clusters |
Man page
Source code
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| plot_tsne_label_by_genes |
Man page
Source code
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| plot_tsne_label_by_multiple_gene_sets |
Man page
Source code
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| plot_tsne_label_by_multiple_gene_sets_with_limited_sampleID |
Man page
Source code
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| plot_tsne_label_by_qc |
Man page
Source code
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| plot_tsne_label_by_sampleID |
Man page
Source code
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| plot_tsne_label_by_selected_sampleID |
Man page
Source code
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| plot_umap_label_by_AUCell_score |
Man page
Source code
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| plot_umap_label_by_a_feature_of_interest |
Man page
Source code
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| plot_umap_label_by_a_signature_gene_set |
Man page
Source code
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| plot_umap_label_by_clusters |
Man page
Source code
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| plot_umap_label_by_genes |
Man page
Source code
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| plot_umap_label_by_multiple_gene_sets |
Man page
Source code
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| plot_umap_label_by_multiple_gene_sets_with_limited_sampleID |
Man page
Source code
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| plot_umap_label_by_qc |
Man page
Source code
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| plot_umap_label_by_sampleID |
Man page
Source code
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| plot_umap_label_by_selected_sampleID |
Man page
Source code
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| plot_variable_genes |
Man page
Source code
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| plot_violin_for_differential_genes |
Man page
Source code
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| plot_violin_for_genes_per_custom_group_of_cells |
Man page
Source code
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| plot_violin_for_marker_genes |
Man page
Source code
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| preprocess_integration |
Man page
Source code
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| preprocess_integration_for_ADT |
Man page
Source code
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| process_cells_annotation |
Man page
Source code
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| remove_clusters |
Man page
Source code
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| remove_unwanted_confounders |
Man page
Source code
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| remove_unwanted_genes_from_variable_gene_set |
Man page
Source code
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| runCombat |
Man page
Source code
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| runDiffusionMap |
Man page
Source code
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| runFA2_ForceDirectedGraph |
Man page
Source code
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| runHarmony |
Man page
Source code
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| runKBET |
Man page
Source code
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| runKNN_Graph |
Man page
Source code
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| runLISI |
Man page
Source code
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| runLiger_online_iNMF |
Man page
Source code
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| runNNMF |
Man page
Source code
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| runPCA |
Man page
Source code
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| runScanorama |
Man page
Source code
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| runSeuratIntegration |
Man page
Source code
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| runSeuratIntegration_with_rpca |
Man page
Source code
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| runSupervised_Harmony |
Man page
Source code
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| runTSNE |
Man page
Source code
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| runUMAP |
Man page
Source code
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| show |
Man page
|
| show,SingCellaR-method |
Man page
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| show,SingCellaR_Int-method |
Man page
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| sub_clusters |
Man page
Source code
|
| subsample_cells |
Man page
Source code
|
