| check_for_polystest | Check SummarizedExperiment for PolySTest Requirements |
| check_stat_names | Check Statistical Test and Comparison Names |
| create_pairwise_comparisons | Create All Pairwise Comparisons |
| FindFCandQlimAlternative | Function to determine "optimal" fold-change and q-value thresholds using a higher criticism method and an FC threshold based on a standard deviation of one |
| get_numthreads | Set number of threads (default is 4) |
| limma_paired | Perform paired limma analysis |
| limma_unpaired | Perform unpaired limma analysis |
| liver_example | Example data set liver_example for PolySTest |
| MissingStats | Calculates the p-values and q-values for missing values in a data frame with columns as samples and rows as features. |
| MissingStatsDesign | Function of calculation of Miss tests. This happens between full groups and thus does not have distinction for pairwise testing. |
| MissValPDistr | Calculate the distribution of missing values |
| permtest_paired | Perform permutation tests |
| perm_unpaired | Perform unpaired permutation tests |
| plotExpression | Plot Expression Profiles |
| plotHeatmaply | Heatmap Visualization with Heatmaply |
| plotPvalueDistr | Plot P-Value Distributions |
| plotRegNumber | Plot Number of Regulated Features |
| plotUpset | Plot UpSet |
| plotVolcano | Plot Volcano Plots for PolySTest results |
| PolySTest_paired | PolySTest for Paired Tests |
| PolySTest_unpaired | PolySTest for unpaired tests |
| RPStats | RPStats Function |
| rp_unpaired | Perform unpaired rank products test |
| set_mfrow | Set Graphics Layout |
| StatsForPermutTest | Calculate statistics for permutation test |
| ttest_paired | Perform paired t-tests |
| ttest_unpaired | Perform unpaired t-tests on two datasets |
| update_conditions_with_lcs | Update Conditions with Longest Common Subsequence |