Man pages for cellGeometry
Geometric Single Cell Deconvolution
| add_noise | Add noise to count data |
| adjust_library_size | Adjust count matrix by library size |
| cellMarkers | Identify cell markers |
| collapse_group | Collapse groups in cellMarkers object |
| comp_heatmap | Compensation heatmap |
| confint.deconv | Confidence Intervals for Deconvolution Models |
| cos_similarity | Gene signature cosine similarity matrix |
| deconvolute | Deconvolute bulk RNA-Seq using single-cell RNA-Seq signature |
| diagnose | Diagnostics for cellMarker signatures |
| fix_bulk | Fix in missing genes in bulk RNA-Seq matrix |
| fix_group | Fix cellMarkers signature with no cell groups |
| gene2symbol | Converts ensembl gene ids to symbols |
| gene_angle | Vector based best marker selection |
| generate_samples | Generate random cell number samples |
| kappa.deconv | Compute condition number of deconvolution model |
| logmean | Mean Objects |
| max_similarity | Maximum similarity between cell types |
| mergeMarkers | Merge cellMarker signatures |
| metric_set | Calculate R-squared and metrics on deconvoluted cell... |
| plot_biasvar | Plot bias-variance decomposition |
| plot_comp | Plot compensation analysis |
| plot_cv | Plot deconvolution lambda cross-validation curve |
| plot_pred | Scatter plot to compare deconvoluted subclasses |
| plot.qqmap | Quantile-quantile plot |
| plot_residuals | Residuals plot |
| plot_set | Scatter plots to compare deconvoluted subclasses |
| plot_tune | Plot tuning curves |
| quantile_map | Quantile mapping function between two scRNA-Seq datasets |
| rank_angle | Rank distance angles from a cosine similarity matrix |
| reduceNoise | Reduce noise in single-cell data |
| residuals.deconv | Extract Deconvolution Residuals |
| rstudent.deconv | Regression Deletion Diagnostics |
| scapply | Single-cell apply a function to a matrix split by a factor |
| scmean | Single-cell mean log gene expression across cell types |
| se | Standard errors of deconvoluted cell counts |
| signature_heatmap | Gene signature heatmap |
| simulate_bulk | Simulate pseudo-bulk RNA-Seq |
| slapply | Apply a function to a big matrix by slicing |
| specificity_plot | Specificity plot |
| spillover_heatmap | Spillover heatmap |
| stack_plot | Stacked bar plot |
| summary.tune_deconv | Summarising deconvolution tuning |
| tune_deconv | Tune deconvolution parameters |
| updateMarkers | Update cellMarkers object |
| violin_plot | Cell subclass violin plot |
