Man pages for jmonlong/scCNAutils
Functions to analyze copy number aberrations in single-cell data
| annotate_cna | Annotate CNAs with gene information |
| annotate_cna_seg | Annotate CN segments |
| auto_cna_call | Automated pipeline to call CNA |
| auto_cna_signal | Automated pipeline to compute CNA signal from scRNA... |
| bin_genes | Merge consecutive genes into expressed bins |
| binGenesC | Bin genes |
| call_cna | Call CNA |
| call_cna_multisamps | Call CNA |
| cnaHMM | Call CNA using a HMM approach |
| convert_to_coord | Convert gene symbols to coordinates |
| define_cycling_cells | Define cycling cells |
| find_communities | Community detection |
| gene_info | Gene information |
| make_metacells | Make metacells |
| merge_samples | Merge expression of multiple samples |
| metacells_cluster | Metacells by clustering within communities. |
| metacells_subsample | Metacells by subsampling within communities. |
| norm_ge | Normalize gene expression |
| norm_ge_tmm | Normalize gene expression using TMM |
| norm_ge_total | Normalize gene expression using total expression |
| plot_aneuploidy | Aneuploidy graph |
| plot_cna | Heatmap of CNA |
| plot_communities | Community graphs |
| plot_heatmap | Heatmap of the CNA scores |
| plot_qc_cells | QC graphs |
| plot_tsne | tSNE graphs |
| plot_umap | UMAP graphs |
| qc_cells | Compute quality control metrics for each cell |
| qc_filter | Filter cells based on QC results |
| read_mtx | Read a trio of genes, barcodes and mtx files. |
| rebin_cov | Re-bin coverage data |
| rm_cv_outliers | Remove outliers based on the coefficient of variation |
| run_louvain | Python wrapper to run Louvain |
| run_pca | Run PCA |
| run_tsne | Run tSNE |
| run_umap | Run UMAP |
| scCNAutils-package | scCNAutils |
| smoothMovingC | Smooth signal |
| smooth_movingw | Moving-window smoothing |
| tmmNormC | Compute the normalization factor |
| tsne_browser | Shiny application to visualize tSNE results |
| umap_browser | Shiny application to visualize UMAP results |
| winsor | Winsorize |
| zscore | Compute Z-score |
