Man pages for kgellatl/SignallingSingleCell
Network Analysis for single cell RNA sequencing Data (sc-RNASeq)
| agg_gene | Normalization |
| analyze_rl_network | Identifies all R / L interactions |
| build_rl_network | Identifies all R / L interactions |
| calc_agg_bulk | Calculate UPM expression values across pData values |
| calc_genestats | Calculate Gene Stats |
| calc_libsize | Calculate Library Size |
| calc_rl_connections | Identifies all R / L interactions |
| cell_cor | Dimension Reduction |
| cell_net | Dimension Reduction |
| cluster_cell_net | Dimension Reduction |
| cluster_sc | Cluster Single Cell |
| construct_ex_sc | Construct Expression Set Class |
| construct_ex_sc_10x | Calculate Library Size |
| detect_doublets | Calculate UPM expression values across pData values |
| dim_reduce | Dimension Reduction |
| edgeRDE | This will run edgeR to find differentially expressed genes.... |
| extract_communities | Identifies all R / L interactions |
| extract_nodes | Identifies all R / L interactions |
| filter_rl_network | Identifies all R / L interactions |
| findDEgenes | This will perform differential expression using edgeR for... |
| findDEmarkers | This will perform differential expression using edgeR to find... |
| flow_filter | Construct Expression Set Class |
| flow_svm | Flow Support Vector Machine |
| id_markers | ID markers |
| id_rl | identify receptors and ligands |
| merge_ex_sc | This will merge pData and fData |
| norm_sc | Normalization |
| plot_barplot | This will create a bar plot |
| plot_density | Plot Density |
| plot_density_ridge | Plot Density |
| plot_dotplot | This will create a bar plot with dots |
| plot_gene_dots | Plot of genes by pData variable |
| plot_go_heatmap | Construct Expression Set Class |
| plot_heatmap | Plots a heatmap |
| plot_rl_summary | Identifies all R / L interactions |
| plot_scatter | Create a Scatter Plot |
| plot_tsne_gene | tSNE Plot on a gene or gene |
| plot_tsne_metadata | tSNE Plot on metadata |
| plot_violin | plot_violin |
| plotViolin | This will create a violin plot |
| plot_volcano | Calculate Library Size |
| pre_filter | Filter Data |
| reduce_cell_net | Dimension Reduction |
| return_agg_gene | Normalization |
| return_markers | Return markers |
| return_subset_genes | Subset Genes |
| save_ggplot | Save plot |
| search_gene | Search Gene |
| subset_ex_sc | This will setset your expression set by some variable in... |
| subset_genes | Subset Genes |
