Man pages for nkurniansyah/Olivia
RNA-seq Analysis
| apply_filters | Filter gene counts matrix by applying various filters |
| compute_quantile_empirical_pvalues | Quantile empirical P-values |
| ENSG00000000003 | Single gene count (ENSG00000000003) |
| filter_by_genes | Filter gene counts matrix by geneID |
| lm_count_mat | Fast linear regression |
| lm_count_mat_emp_pval | Wrapper function for differential expression analysis |
| lm_count_mat_perm_pval | Wrapper function for permutation differential expression... |
| lm_count_mat_permute | Fast linear regression |
| lm_mult_count_mat_emp_pval | Wrapper function for differential expression analysis for... |
| log_add_0.5 | Log add half |
| log_add_min | Log add minimum value |
| log_replace_half_min | Log replace half min |
| log_transform_count | Applying log transform on a matrix of gene counts |
| median_normalization | Median Normalization |
| mult_lm_count_mat | Fast linear regression for multiple exposure |
| permutation_pvalues | Permutation P-values |
| permute_resids_trait | Residual permutation |
| permute_resids_trait_cor | Power Simulations |
| phenotype | Simulated phenotypes. |
| residual_plot | Title Residual Plot |
| rnaseq_count_matrix | Raw gene count matrix |
| summarize_phenotypes | Title Summarize phenotypes |
| summary_phenotype | Title Summary phenotype |
| violin_plot | Title Violin plot |
| volcano_plot | Title Volcano plot |
