Man pages for GrigoriiNos/rimmi.rnaseq
Set of functions for genomics data analysis
| add_hash | Merge cell hashcoding demultiplexed data with GEX Seurat 3... |
| add_vdj | Merge clonotype and isotype data to GEX Seurat object |
| all.genes.withGO | Get all genes with partiular GO |
| annotate_markers | Annotation for the cell markers. |
| Cell.cell.corheatmap | heatmap for cell-cell correlation matrix |
| cellphone_for_seurat | cell-cell interaction analysis using method CellPhoneDB |
| clean_spmat | Run Velocyto analysis on your Seurat2 object |
| clonotypes_summary | Gives you a summary of your clonotypes |
| dot_plot_topXgenes | Make a dot plot for all your markers |
| Gene.gene.corheatmap | heatmap for gene-gene correlation matrix |
| geom_split_violin | ggplot extension for split violin plot |
| get_emb | Run Velocyto analysis on your Seurat2 object |
| Hglm.deg | apply DEG with multiple glms on Seruat object with case... |
| HTODemux | HTODemux in house modified Seurat::HTODemux for identifiyng... |
| hto.heatmap | hto heatmap |
| lib.qc_plot | Plot clusters in 2 umaps with the point size corresponting to... |
| list.to.table | unite list of deg table |
| markers_to_xls | getting your markers into the excel shpreadsheet |
| merge_loom | Merge two loom files into one and produce rvel.cd |
| preprocess_loom | Run Velocyto analysis on your Seurat2 object |
| pseudo.bulk.DEG | apply DESeq for DEG pseudo bulk collapsed samples |
| pull_vdj | Merge clonotype and isotype data to GEX Seurat object |
| quantify_genesets | This function allows you to calculate an average expression... |
| query_heatmap | heatmap genes with certain function |
| rank_clonotypes | Rank clonotypes based of the spread in GEX space |
| save.plot_grid | save multiple gg plots in pdf |
| Seurat2_velocyto | Run Velocyto analysis on your Seurat2 object |
| SplitObject | Splits object into a list of subsetted objects. |
| unarchive_10x | Prepare 10x v3 out files files for Seurat 2 |
| volcano_pl | plot volcano plot 2 |
| volcano_pl2 | plot volcano plot 2 |
