| aggregate_counts | Aggregates reads counts from SNPs to transcript and... |
| analyze_imbalance_vs_counts | Reads ratios from the file and calculate gini indexes |
| analyze_NPC_pulled_clones | Runs analysis for NPCs: pull clones, look at SDs |
| analyze_NPC_var | Runs analysis for NPCs |
| analyze_rin | Analyze rin vs. sd for all individuals for a given tissue |
| analyze_sd_by_threshold | Reads counts, apply thresholds, plot distributions |
| analyze_sd_for_tissues | Analyze sd distributions for all individuals for all tissues |
| analyze_sd_MAE_BAE | Reads ratios from the file and analyze standard deviations |
| compare_high_vs_low_samples | Compares sample with high and low ratio variability |
| compare_same_ind_diff_tissues | Compare same individuals in different tissues |
| generatePlots | Generate variatility plots for a given tissue |
| get_ASE_files_list | Gets a list of files containing ASE information for a given... |
| get_classification | Returns tissue classification with Ensembl id column |
| get_counts_for_sample | Gets a table with reference and allelic counts for a given... |
| get_counts_statistics | Calculates mean, sd, CV, CV2 for each gene |
| get_full_name | Gets full tissue name from a short name |
| get_individuals_subset | Outputs sample ids for individuals with high or low ratios... |
| get_ratio_sd | Get allelic ratio's standard deviation for a tissue,... |
| get_ratios_sample | Gets ratios for a given tissue |
| get_rin_correlations_for_tissues | Produce plot with RIN vs SD(allelic_ratio) for several... |
| get_samples_tissues | Reads ratios from the file, subsamples and makes a plot |
| get_sd_ratios | Calcultates SDs for allelic ratios |
| get_short_name | Gets short tissue name from a full name |
| get_tissue_code | Gets tissue code from a short name |
| list_of_samples_with_ratios | Run ratios analysis for NPCs |
| load_counts | Loads counts from Rda |
| load_Gtex_data | Coverts GTEx data from 3 files (downloaded from GTEx website)... |
| make_plot_for_NPC | Run ratios analysis for NPCs |
| measure | Calculates CVs for "observed" BAE and all genes from counts... |
| plot_CV2_vs_mean | Plots CV2 versus mean |
| plot_density_ratio_per_individual | Reads ratios from the file and makes a plot of density,... |
| plot_density_ratio_per_individual_all_tissues | Plot ratio densities for all tissues |
| plot_one | Plots boxplots for ranges |
| plot_two | Plots scatterplots |
| process_to_counts | Proccesses GTEx counts and merges counts statistics with... |
| read_counts | Reads counts for a given tissue |
| read_counts_and_calc_ratios | Reads counts for a given tissue, aggregates them and puts... |
| read_counts_and_merge_samples | Reads counts for a given tissue, aggregates them and puts... |
| read_ratios | Reads ratios for a given tissue |
| save_counts | Reads and saves counts for a given tissue |
| save_counts_tissues_of_interest | Saves counts to files for the tissues of interest |
| save_Gtex_data_by_tissue | Saves selected tissues counts to .Rda files |
| save_ratios | Reads and saves ratios for a given tissue |
| save_ratios_tissues_of_interest | Saves ratios to files for the tissues of interest |
| simulate_ratios | Makes boxplots for SDs |
| subset_and_get_ratio | Pulls data and gets allelic ratios |
| subsetGtexData | Subsets GTEx ExpressionSet to a given tissue |
| variation_analysis_for_subset | Do variation analysis for samples with moderate sd values |
| zscores_heatmap | Convert normalized counts to z-scores and plot heatmaps |
