| add_avg_beta | Add beta-values to table with means of M-values |
| assoc | Association test between two variables |
| binary_str_lengths | Calculate lengths of each string of ones in a binary vector... |
| combine_directional_pvalues | Directionally combine p-values |
| cor_by_grp | Correlation test in each group |
| correct_null_distribution | Correct null distribution |
| deseq2_contrasts | Apply DESeq2's DESeq, results, and lfcShrink to one or more... |
| deseq2_cor | Apply DESeq2's DESeq, results, and lfcShrink to one or more... |
| deseq2_find_all_markers | Find markers by DESeq2's pairwise wald tests |
| deseq2_find_markers | Find markers by DESeq2's pairwise wald tests |
| deseq2_lrt | Apply DESeq2's DESeq, results, and lfcShrink to one or more... |
| dream_contrasts | Apply variancePartition's dream to one or more contrasts,... |
| dream_cor | Apply variancePartition's dream to one or more contrasts,... |
| dream_ftest_contrasts | Apply variancePartition's dream to one or more contrasts,... |
| dream_ftest_pairwise | Perform dream's moderated F-test for all pairwise... |
| edger_contrasts | Apply edgeR's glmQLFit or glmFit, glmQLFTest, glmLRT, or... |
| edger_ftest_contrasts | #' Apply edgeR's glmQLFit or glmFit, glmQLFTest, glmLRT, or... |
| enrichFRY | enrichFRY |
| ezbacon | Apply 'bacon' to z-scores |
| ezgetBM | Get gene annotation from biomart |
| ezumap | UMAP plot of first two dimensions |
| filter_valids | Filter features |
| find_mode | Mode estimation of a continuous variable |
| find_pc_curve_elbow | Identify and plot the elbow point of the PC curve |
| find_top_cluster_markers | Find top cluster markers |
| gsub0 | Gsub with empty replacement |
| hclust_and_heat | Hierarchical Clustering & visualization by heatmap |
| hclust_in_grp | Hierarchical Clustering in each group |
| impute_normal | Impute missing values by random numbers drawn from a normal... |
| limma_find_all_markers | Find markers for each group by limma's pairwise moderated... |
| limma_find_markers | Find markers by limma's pairwise moderated t-tests |
| limma_ftest_contrasts | Apply limma's lmFit, contrasts.fit, & eBayes to one or more... |
| limma_ftest_pairwise | Perform limma's moderated F-test for all pairwise comparions,... |
| limma_treat_find_all_markers | Find markers for each group by limma's pairwise moderated... |
| limma_treat_max | Apply limma's lmFit, contrasts.fit, & treat to one or more... |
| limma_treat_pairwise | Perform limma's treat for all pairwise comparions, and return... |
| limma_trend_plot | Mean-variance trend plot |
| make_file_links | Make file links for R Markdown |
| make_gsea_barplot | Make a barplot for GSEA results |
| make_gsea_cnet | Make cnets plot for a list of GSEA results |
| make_piechart | Make a pie chart |
| make_smpdb_glist | Make a feature list for SMPDB pathways. |
| map_by_adist | Map two character vectors by approximate string distances |
| map_t2g | Map pathway term to gene IDs to another ID type |
| match_met_nms | Match names of chemicals |
| multi_assoc | Association tests for two groups of variables |
| multi_enrichFRY | multi_enrichFRY |
| multi_pval2z | Convert multiple columns of p-values to Z-scores |
| multi_pval2zlist | Convert multiple columns of p-values to list of named and... |
| multivariate_pc_regression | Multivariate regression for meta variables and principal... |
| parse_cutadapt_logs | Parse cutadapt log files |
| parse_featureCounts_logs | Parse featureCounts log file |
| parse_kallisto_logs | Parse kallisto log files |
| parse_star_logs | Parse star log files |
| pc_assoc | Association tests for meta variables and principal components |
| plot_pvals | Plot p-values |
| pval2z | Convert p-values to Z-scores |
| rankprod | Rank products of a matrix where larger statistics have... |
| ranksum | Rank sum of a matrix where larger statistics have stronger... |
| revcomp | converts a DNA sequence into its reverse-complement... |
| sample_bsgenome_regions | Rand seq |
| select_top | Select equal numbers of top features from the topTable |
| select_top_2sided | Select equal numbers of top features from the topTable |
| signed_rankprod | Signed rank products of a two column matrix where larger... |
| signed_ranksum | Signed rank sum of a matrix where larger statistics have... |
| sub0 | Sub with empty replacement |
| update_function_arguments | Change the formal arguments of a function |
| venn_fisher_test | Fisher exact test for 2-way Venn |
| z_2prop_pooled | Two-proportion z-test (pooled) for non-zero null |
| zscore_prod | Z-score products of a two column matrix where larger scores... |
