Man pages for xuranw/MuSiC
Multi-subject single cell deconvolution
| Abs_diff_multi | Plot heatmap of Absolute difference between estimated and... |
| Anova_info | ANOVA Test for each gene |
| Boxplot_Est | Boxplot of estimated cell type proportions |
| bulk_construct | Construct artificial bulk tissue expression from single cell... |
| CellTotal.df | Compare cell type specific total expression (library size)... |
| Eval_multi | Evaluate estimation methods |
| Eval_sim_boxplot | Evaluate simulation results by boxplots |
| fpkmToTpm | Calculate fpkm to tpm |
| get_upper_tri | Get upper triangle matrix |
| Jitter_Est | Jitter plot of estimated cell type proportions |
| music2_prop | MuSiC2_Deconvolution |
| music2_prop_toast | MuSiC2 Deconvolution with TOAST |
| music2_prop_t_statistics | MuSiC2 Deconvolution with T Statistics |
| music.basic | Estimate cell type proportion with MuSiC and NNLS |
| music.basic.ct | Estimate cell type proportion with MuSiC and NNLS |
| music_basis | Prepare Design matrix and Cross-subject Variance for MuSiC... |
| music_Design.matrix | Cell type specific library size |
| music.iter | Scaling bulk data and signature matrix and estimate cell type... |
| music.iter.ct | Scaling bulk data and signature matrix and estimate cell type... |
| music_M.theta | Cross-subject Mean of Relative Abudance |
| music_prop | MuSiC Deconvolution |
| music_prop.cluster | MuSiC Deconvolution with Clusters |
| music_S | Cell type specific library size |
| music_Sigma | Cross-subject Variance of Relative Abundance |
| music_Sigma.ct | Cross-subject Covariance of Relative Abundance |
| music_Theta | Subject and cell type specific relative abundance |
| my.log | log transformation with regulation |
| my.rowMeans | Calculate Row Means with NA remove |
| my.sqrt | Calculate square root of all values |
| plotCellTotal.two | Plot the cell type specific library size of 2 single cell... |
| Prop_comp_multi | Plot heatmap of real and estimated cell type proportions |
| Prop_convert | Convert list of real and estimated cell type proportions to... |
| Prop_heat_Est | Heatmap of estimated cell type proportions |
| relative.ab | Calculate relative abundance |
| Relative_gene_boxplot | Boxplot of relative abundance |
| Scatter_multi | Plot Scatter plot of real and estimated cell type proportions |
| Twocelltype.Generator | Simulate Single cell read counts |
| Weight_cal | Calculate weight with cross-subject variance for each cell... |
| weight.cal.ct | Calculate weight with cross cell type covariance |
