Man pages for compbiomed/BatchQC
Batch Effects Quality Control Software
| batch_correct | Batch Correct This function allows you to Add batch corrected... |
| batch_design | This function allows you to make a batch design matrix |
| batch_indicator | Batch and Condition indicator for signature data |
| BatchQC | Run BatchQC shiny app |
| batchqc_explained_variation | Returns a list of explained variation by batch and condition... |
| bladder_data_upload | Bladder data upload This function uploads the Bladder data... |
| check_valid_input | Helper function to save variables as factors if not already... |
| color_palette | Color palette |
| combat_correction | Combat Correction This function applies combat correction to... |
| combat_seq_correction | Combat-Seq Correction This function applies combat-seq... |
| confound_metrics | Combine std. Pearson correlation coefficient and Cramer's V |
| cor_props | This function allows you to calculate correlation properties |
| counts2pvalue | This function calculates p-values for each gene given counts,... |
| covariates_not_confounded | Returns list of covariates not confounded by batch; helper... |
| cramers_v | This function allows you to calculate Cramer's V |
| DE_analyze | Differential Expression Analysis |
| dendrogram_alpha_numeric_check | Dendrogram alpha or numeric checker |
| dendrogram_color_palette | Dendrogram color palette |
| dendrogram_plotter | Dendrogram Plot |
| EV_plotter | This function allows you to plot explained variation |
| EV_table | EV Table Returns table with percent variation explained for... |
| get.res | Helper function to get residuals |
| goodness_of_fit_DESeq2 | This function calculates goodness-of-fit pvalues for all... |
| heatmap_num_to_char_converter | Heatmap numeric to character converter |
| heatmap_plotter | Heatmap Plotter |
| nb_histogram | This function creates a histogram from the negative binomial... |
| nb_proportion | This function determines the proportion of p-values below a... |
| normalize_SE | This function allows you to add normalized count matrix to... |
| PCA_plotter | This function allows you to plot PCA |
| plot_data | This function formats the PCA plot using ggplot |
| preprocess | Preprocess assay data |
| process_dendrogram | Process Dendrogram |
| protein_data | Protein data with 39 protein expression levels |
| protein_sample_info | Batch and Condition indicator for protein expression data |
| pval_plotter | P-value Plotter This function allows you to plot p-values of... |
| pval_summary | Returns summary table for p-values of explained variation |
| ratio_plotter | This function allows you to plot ratios of explained... |
| signature_data | Signature data with 1600 gene expression levels |
| std_pearson_corr_coef | Calculate a standardized Pearson correlation coefficient |
| summarized_experiment | This function creates a summarized experiment object from... |
| variation_ratios | Creates Ratios of batch to variable variation statistic |
| volcano_plot | Volcano plot |
