Man pages for SlideCNA
Calls Copy Number Alterations from Slide-Seq Data
| bin | Subfunction of bin_metadata() for expression/positional... |
| bin_metadata | Spatio-molecular binning of relative expression intensities |
| center_rm | Center expression intensities |
| clone_so | Add clone information to meta data of seurat object and bin... |
| cnv_heatmap | Plot CNV scores on a heat map |
| dat_to_long | Convert data to long format and add in metadata |
| find_cluster_markers | Find and plot top n DEGs per cluster |
| find_go_terms | Find and plot top n GO-enriched terms per cluster |
| get_num_clust | Find optimal number of clusters |
| long_to_bin | Convert to wide bin x genes + metadata format |
| make_seurat_annot | Creation of Seurat object |
| make_so_bin | Make a binned version of a Seurat object |
| mean_cnv_plot | Plot mean CNV scores per bin and per chromosome |
| mode | Subfunction of long_to_bin() that finds mode of vector/column |
| plot_clones | Plot cluster/clone information |
| prep | Infercnv-based preparation of relative gene expression... |
| prep_cnv_dat | Prepare data for CNV heat map |
| quantile_plot | Plot CNV score quantiles per bin and per chromosome |
| reexports | Pipe |
| ref_adj | Adjust for Reference (Normal) Beads |
| run_enrichr | Subfunction to get significantly enriched GO terms given a... |
| run_slide_cna | Run SlideCNA workflow |
| scalefit | Subfunction for scale_nUMI that normalizes a given bin for... |
| scale_nUMI | Scale for nUMI (UMI Count) to generate CNV scores |
| SpatialPlot | Spatial plots of meta data |
| weight_rollmean | Expressional smoothing along a chromosome using a weighted... |
| weight_rollmean_sub | Subfunction of weight_rollmean |
