Man pages for ycl6/scRUtils
Single-Cell Sequencing Analysis Utilities
| add_label | Add labels to reduced dimension plots |
| check_and_liftCC | Check and lift cell type compositions between 2 CellChat... |
| choosePalette | Choose discrete colours |
| data-dbl_results | findDoubletClusters results from a simulated single-cell... |
| data-phases_assignments | cyclone results from a simulated single-cell RNA-seq dataset |
| data-res_deseq2 | A DESeq2 DESeqResults produced from the pasilla dataset |
| data-res_edger | A edgeR TopTags object produced from the pasilla dataset |
| data-sce | A processed simulated single-cell RNA-seq dataset |
| discrete_colors | Discrete palettes |
| exportResList | Export results from findMarkers, edgeR or DESeq2 to tsv |
| fig | Change repr.plot.* behaviour |
| geom_parallel_sets_labs | Add nudged labels in a parallel sets diagram |
| getDEGs | Retrieve differentially expressed genes from edgeR or DESeq2... |
| get_Legend | Retrieve the legend of a plot |
| getMarkers | Retrieve marker genes from a 'findMarkers' output DataFrame |
| netVis_heatmap | Visualization of network using heatmap |
| plotBox | Create a boxplot of expression values |
| plotCyclone | Plot G2M against G1 scores from 'cyclone' results |
| plotEnrichR | Visualise Enrichr results as barplots |
| plotExprsFreqVsMean | Plot expression frequency against mean counts |
| plotParallel | Create a 2-variable parallel sets diagrams |
| plotProjection | Colour cells by a feature in a 2-dimension representation |
| plotProjections | Colour cells by a feature in two 2-dimension representation... |
| plotqcDoubletClusters | Create QC plots from 'findDoubletClusters' output |
| plotReducedDimLR | Show ligand-receptor gene expression in reduced dimensions |
| plotSilhouette | Plot distribution of approximate silhouette widths |
| plotVariableFeature | Plot variance modelling results |
| plotVarianceVsMean | Plot logcounts variance against logcounts mean |
| printEnrichR | Export results from Enrichr to tsv |
| printMarkerStats | Print marker gene stats from 'findMarkers' output |
| runEnrichR | Perform enrichR analysis on results from findMarkers, edgeR... |
| scRUtils-package | scRUtils package |
