Man pages for szymczak-lab/QCnormSE
Quality Control of Normalized Gene Expression Data
| aggregate_by_new_id | Aggregate expression values based on new identifiers |
| calculate_mds_pca | MDS or PCA |
| check_batch_effects | Check for batch effects |
| check_sex | Sex check |
| combine_se_objects | Merge SummarizedExperiments objects |
| define_batches | Define batches based on scan date |
| detect_duplicated_samples | Identification of duplicated samples |
| extract_detection_pvalue | Extract detection P value |
| extract_geo_characteristics | Extract GEO information |
| extract_scan_date | Extract scan date |
| get_geo_data | Export gene expression data sets from GEO |
| info.sex.genes | Genes on the X and Y chromosome |
| log_transform | Log transformation |
| normalize_counts | Normalize raw read counts of RNA-seq experiments |
| plot_distribution | Plot distribution of expression values for each sample |
| plot_heatmap | Plot heatmap |
| plot_mds_pca | MDS or PCA plot |
| plot_mds_pca_2d | MDS or PCA plot (2D) |
| remove_genes | Remove genes based on different criteria |
| remove_samples | Remove samples based on different criteria |
| se.gene | Example data set (microarray, gene level) |
| se.probeset | Example data set (microarray, probeset level) |
