| add_se_cols | Add column to toptab with standard errors |
| add_zcols | Add column to toptab with z-stats |
| batch2design | Transform factor vector into design matrix |
| clean_filenames | Alter names to valid filenames |
| combine_pvalues | Combine p-values of a feature over multiple p-value columns... |
| df_signif | Apply 'signif' function to numeric columns of data frames |
| ezcamerapr | A wrapper function for 'cameraPR' with output to Excel |
| ezcor | Test correlation of each row of an object to a phenotype... |
| ezebayes | Wrapper for limma's eBayes function that also allows for... |
| eztoptab | Wrapper for limma topTable function |
| fc2ratio | Transform fold-change (FC) into a ratio |
| fisher_enrichment | Fisher Exact Test of gene set enrichment with output to Excel |
| g_index | Create object with indices of genes per gene set |
| gmat2gmt | Transform analyte-by-pathway matrix into list compatible with... |
| grep_cols | Find p-value or stat columns in table |
| grp_means | Calculate group means per feature |
| limma_contrasts | Apply limma's lmFit, contrasts.fit, & eBayes to one or more... |
| limma_cor | Test correlation of each row of object to phenotype using... |
| limma_tost | Two one-sided test procedure with 'limma' for statistical... |
| logfc2fc | Transform a log2 fold-change to a fold-change |
| map_glist | Map pathway list gene IDs to another ID type |
| multi_cor | Test correlation of each row of an object to each column of... |
| multi_fisher_enrichment | Fisher Exact Test of gene set enrichment with multiple... |
| multiTopTab | Combine one or more toptables extracted from linear model fit |
| prop_changed | Calculate proportion of changed features per pathway |
| read_gmt | Read gene set file with GMT extension to a list |
| read_linked_xl | Read Excel XLSX file with links to CSVs |
| roast_contrasts | Test contrasts of gene sets between groups using rotation... |
| roast_cor | to Excel |
| roast_multi_cor | to Excel |
| roast_two2one_tailed | Convert roast two-tailed results to one-tailed |
| sim_fisher | Apply 'fisher_enrichment' to simulated data |
| SMPDB2G | Transform SMPDB protein and/or metabolite pathway data frames... |
| two2one_tailed | Convert 2-tailed into 1-tailed p-values |
| write_gmt | Write gene set file with GMT extension from a list |
| write_linked_xl | Write Excel XLSX file with links to CSVs |
| xl_pwys | Make XL data frame for 'writexl' |
