Man pages for Lian-Lab/LIANLAB
To integrate analysis methods and simplify analysis process
| cluster_annotate | annotate the celltype for cluster in the seurat.obj |
| Get_ave_heatmap | To draw the average expression of the cluster |
| Get_BASIC_drawing | To get basic drawing, including t-SNE, split figure and... |
| Get_Cor | Compare the correlations between clusters in one/two... |
| Get_for_integrated | To get seurat.obj for integrated |
| Get_Genes | Find out if the gene is in the object |
| Get_GK1 | Batch/Specify cell population for GO and KEGG analyse |
| Get_GK2 | GO and KEGG analyse of the result between two clusters |
| Get_GK_genes | Integrated GO/KEGG pathways gene |
| Get_GSEA | Title |
| Get_HM_gene_change | To change the genes from human/mouse to mouse/human |
| Get_integrated | To integrate different batch seurat.obj together |
| Get_monocle | To analyse the seurat.obj easily |
| Get_percentplot | Get percentage of seurat.obj |
| Get_percentplot_split | Get percentage of seurat.obj, which has more than one samples |
| Get_samples_to_group | To split the cells to 'group' by 'samples' |
| Get_Scatterplot1 | to show genes like FACS with colors |
| Get_Scatterplot2 | To show the corralations between two genes |
| Get_Seurat | To get seurat.obj easily |
| Get_singleR | Title |
| GO_diff_barplot | This function is used to plot different GO terms between two... |
| GSVA_difference | This function is used to perform GSVA analysis between two... |
| GSVA_find_gs_markers | To find geneset markers of each cluster |
| GSVA_pheatmap | This function is used to perform GSVA analysis |
| GSVA_score_insert | Insert pathway score into the seurat.obj |
| HTO_get_singlet | Citeseq divide HTOtag |
| list-class | List with colors |
| myfeatureplot | Featureplot for genes and split by samples, group and so on. |
| myfindmarkers | To get the top DE gene of cluster |
| myGO_KEGG | GO and KEGG analyse for the DEG |
| myreplace_ident | This function is used to replace the cluster idents in target |
| myvolcano | Volcano for DE genes. |
| plot_violin_manual | plot the stacked violinplot of single cell RNAseq data |
| See_mRNA | To see the distribution of the number of genes |
| stacked_violin_plot | This function is used to plot the stacked violinplot of... |
| test_package | To test the package need |
| top_m | Get DE genes in ave_logFC |
| top_up_down_m | Get DE genes in ave_logFC |
