Man pages for supatt-lab/SingCellaR
SingCellaR: an integrative analysis tool for single-cell RNA sequencing (scRNA-seq) data
| add_cell_cycle_genes_score | Add the cell cycle gene scores into the cell metadata |
| Build_AUCell_Rankings | Building AUCell gene rankings |
| Build_AUCell_Rankings_Fast | Fast building AUCell gene rankings |
| clustering_KMeansOnKNN_Graph | Run K-Means clustering on the KNN-graph |
| DoubletDetection_with_scrublet | DoubletDetection_with_scrublet |
| export_marker_genes_to_table | Export identified marker genes to table. |
| filter_cells_and_genes | Filter out cells and genes |
| findMarkerGenes | Identify marker genes for each cluster. |
| get_cells_annotation | Get cell annotation |
| getCellsFromClusters | Get cell names from selected clusters. |
| get_clusters | Get cluster information |
| get_dfm.result | Get diffusion map analysis result |
| get_dir_path_10x_matrix | Get path directory of 10x data |
| get_fa2_graph.layout | Get FA2 graph-layout |
| get_genes_metadata | Get gene's metadata |
| get_gmtGeneSets | Get gene sets from GMT file |
| get_knn_graph.graph | Get graph from KNN-graph analysis result |
| get_knn_graph.layout | Get graph-layout from KNN-graph analysis result |
| get_lsi.result | Get LSI analysis result |
| get_marker_genes | Get marker genes information |
| getMarkerGenesInfo | Get marker genes information for any selected cluster. |
| get_nnmf.result | Get NNMF analysis result |
| get_normalized_umi | Get normalized UMI count matrix |
| get_pca.result | Get PCA analysis result |
| get_regressout_log_data | Get regressed out log-scaled matrix |
| get_sample_uniq_id | Get unique sample ID |
| get_tsne.result | Get tSNE analysis result |
| get_umap.result | Get UMAP analysis result |
| get_umi_count | Get UMI count matrix |
| get_variable_genes_basic | Identified variable genes by using the standard mean of gene... |
| get_variable_genes_by_fitting_GLM_model | Identified variable genes by fitting the GLM model using mean... |
| get_variable_genes_for_integrative_data_by_fitting_GLM_model | Identified variable genes for the integrative samples. The... |
| identifyClusters | Cell cluster identification |
| identifyDifferentialGenes | Differential gene expression analysis |
| identifyDifferentialGenes_for_all_clusters | Identify differentially expressed genes for all identified... |
| identifyDifferentialGenes_in_a_cluster_vs_the_rest_of_clusters | Identify differentially expressed genes between a selected... |
| identifyDifferentialGenes_in_multiple_clusters_vs_the_rest_of_clusters | Identify differentially expressed genes between multiple... |
| identifyGSEAPrerankedGenes | Identify GSEA preranked genes |
| identifyGSEAPrerankedGenes_for_all_clusters | Identify GSEA's preranked genes for all identified clusters |
| identifyGSEAPrerankedGenes_in_a_cluster_vs_the_rest_of_clusters | Identify GSEA's preranked genes for a selected cluster vs the... |
| identify_potentially_merging_clusters | Identify the clusters that potenntially can be merged. |
| listAvailableGeneSets | List of available gene sets |
| load_gene_expression_from_a_file | Load gene expression from a file |
| load_matrices_from_cellranger | Load 10X sparse data matrices provided by the Cell Ranger... |
| merge_clusters | Merged clusters |
| normalize_UMIs | Normalisation |
| plot_3D_knn_graph_label_by_a_signature_gene_set | Plot KNN-Graph trajectory in 3D with the gene expression of a... |
| plot_3D_knn_graph_label_by_clusters | Plot KNN-Graph trajectory in 3D with the cluster name |
| plot_3D_knn_graph_label_by_gene | Plot KNN-Graph trajectory in 3D with the gene expression of... |
| plot_bubble_for_genes_per_cluster | Plot bubble-plot for gene expression per cluster |
| plot_bubble_for_genes_per_custom_group_of_cells | Plot bubble-plot for gene expression per custom group of... |
| plot_cells_annotation | Plot cell annotation |
| plot_diffusionmap_label_by_clusters | Plot diffusion map with identified clusters |
| plot_diffusionmap_label_by_genes | Plot diffusion map with gene expression |
| plot_diffusionmap_label_by_multiple_gene_sets | Plot diffusion map with the expression of multiple gene sets |
| plot_forceDirectedGraph_label_by_a_feature_of_interest | Plot force-directed graph with a feature of interest |
| plot_forceDirectedGraph_label_by_a_signature_gene_set | Plot force-directed graph with the expression of a gene set |
| plot_forceDirectedGraph_label_by_AUCell_score | Plot force-direct graph with AUCell score |
| plot_forceDirectedGraph_label_by_clusters | Plot force-directed graph with identified clusters |
| plot_forceDirectedGraph_label_by_genes | Plot force-directed graph with gene expression |
| plot_forceDirectedGraph_label_by_multiple_gene_sets | Plot force-directed graph with the expression of selected... |
| plot_forceDirectedGraph_label_by_multiple_gene_sets_with_limited_sampleID | Plot force-directed graph with the expression of multiple... |
| plot_forceDirectedGraph_label_by_qc | Plot force-directed graph with the QC information |
| plot_forceDirectedGraph_label_by_sampleID | Plot force-directed graph with the sampleID |
| plot_forceDirectedGraph_label_by_selected_sampleID | Plot force-directed graph with selected sampleIDs |
| plot_heatmap_for_differential_genes | Plot heatmap for differential genes |
| plot_heatmap_for_fGSEA_all_clusters | Plot heatmap for GSEA for all comparisons |
| plot_heatmap_for_marker_genes | Plot heatmap for identified marker genes |
| plot_jaccard_similarity_among_clusters | Plot jaccard similar across indetified clusters |
| plot_PCA_Elbowplot | Plot PCA's elbow plot |
| plot_ShortestPath_on_3D_knn_graph | Plot the shortest-path on the 3D KNN-Graph |
| plot_ShortestPath_on_forceDirectedGraph_label_by_clusters | Plot the shortest-path on the force-directed graph with... |
| plot_tsne_label_by_a_feature_of_interest | Plot TSNE and display only the feature of interest |
| plot_tsne_label_by_a_signature_gene_set | Plot TSNE with the expression of selected gene set |
| plot_tsne_label_by_AUCell_score | Plot TSNE with AUCell score |
| plot_tsne_label_by_clusters | Plot TSNE with identified clusters |
| plot_tsne_label_by_genes | Plot TSNE with gene expression |
| plot_tsne_label_by_multiple_gene_sets | Plot TSNE with the expression of multiple gene sets |
| plot_tsne_label_by_multiple_gene_sets_with_limited_sampleID | Plot TSNE with the expression of multiple gene sets on... |
| plot_tsne_label_by_qc | Plot TSNE with QC information |
| plot_tsne_label_by_sampleID | Plot TSNE with sampleID information |
| plot_tsne_label_by_selected_sampleID | Plot TSNE and show only selected sampleID |
| plot_umap_label_by_a_feature_of_interest | Plot UMAP and display only the feature of interest |
| plot_umap_label_by_a_signature_gene_set | Plot UMAP with the expression of selected gene set |
| plot_umap_label_by_AUCell_score | Plot UMAP with AUCell score |
| plot_umap_label_by_clusters | Plot UMAP with identified clusters |
| plot_umap_label_by_genes | Plot UMAP with gene expression |
| plot_umap_label_by_multiple_gene_sets | Plot UMAP with the expression of multiple gene sets |
| plot_umap_label_by_multiple_gene_sets_with_limited_sampleID | Plot UMAP with the expression of multiple gene sets on... |
| plot_umap_label_by_qc | Plot UMAP with QC information |
| plot_umap_label_by_sampleID | Plot UMAP with sampleID |
| plot_umap_label_by_selected_sampleID | Plot UMAP and display only selected sampleIDs |
| plot_UMIs_of_HouseKeepingGenes | Plot UMIs of house keeping genes |
| plot_UMIs_vs_Detected_genes | Plot UMI count vs detected genes |
| plot_variable_genes | Plot highly variable genes |
| plot_violin_for_differential_genes | Plot violin-plot for differential genes |
| plot_violin_for_genes_per_custom_group_of_cells | Plot violin-plot for gene expression per custom group of... |
| plot_violin_for_marker_genes | Plot violin-plot for marker genes |
| preprocess_integration | Preprocessing for data integration |
| preprocess_integration_for_ADT | Preprocessing for ADT |
| process_cells_annotation | Process all cells annotation |
| remove_clusters | Remove clusters |
| remove_unwanted_confounders | Removing unwanted confounders using limma |
| remove_unwanted_genes_from_variable_gene_set | Remove unwanted genes from identified list of variable genes |
| Run_AUCell | Run AUCell |
| runCombat | Run combat integration |
| runDiffusionMap | Diffusion map analysis |
| runFA2_ForceDirectedGraph | ForceAtlas2 analysis |
| Run_fGSEA_analysis | Run GSEA analysis |
| Run_fGSEA_for_a_selected_cluster_vs_the_rest_of_clusters | Run GSEA analysis for a selected cluster vs the rest of... |
| Run_fGSEA_for_multiple_comparisons | Run GSEA analysis for multiple comparisons |
| runHarmony | Run harmony integration |
| runKBET | kBET analysis |
| runKNN_Graph | K-nearest neighbor graph analysis |
| runLiger_online_iNMF | Run runLiger_online_iNMF integration (see also... |
| runLISI | LISI analysis |
| runNNMF | NNMF analysis |
| runPCA | PCA analysis |
| runScanorama | Run scanorama integration |
| runSeuratIntegration | Run Seurat integration |
| runSeuratIntegration_with_rpca | Run Seurat integration using reciprocal PCA (RPCA) |
| runSupervised_Harmony | Run supervised harmony integration |
| runTSNE | TSNE analysis |
| runUMAP | UMAP analysis |
| show-methods | show method for SingCellaR |
| SingCellaR | The SingCellaR Class The SingCellaR object stores all of... |
| sub_clusters | Extracting selected clusters. |
| subsample_cells | Subsample cells from the whole data set |
| TargetSeq_filter_cells_and_genes | TargetSeq processing for filtering out cells and genes |
| TargetSeq_load_cell_metadata | Loading cell metdata from TARGET-Seq analysis |
| TargetSeq_plot_cells_annotation | Plot cell annotation for Target-Seq data |
| TargetSeq_process_cells_annotation | Target-Seq processing for cell annotation |
