Man pages for jcalendo/coriell
Convenience Functions for Bioinformatics
| associate_components | Calculate associations between variables and principal... |
| clamp | Limit values to a given range |
| clr | Centered Log-ratio transformation |
| colmean | Give means of rows of matrix based on column grouping... |
| dfs2se | Convert a list of differential expression data.frames to a... |
| distinct_rgb_palette | Generate a distinct RGB color palette |
| edger_to_df | Convert EdgeR results object to a data.frame |
| env2global | Extract variable from an environment and remove that... |
| exact_cor_test | Perform and exact correlation test on every row of a matrix |
| geometric_mean | Geometric mean of a vector |
| get_axis_limits | Get the axis limits of a ggplot2 object |
| GSE161650_de | Differential expression results from GSE161650 |
| GSE161650_lc | Normalized log2 counts from GSE161650 |
| horvath_age | Transform ages using Horvath's method |
| impute | Perform simple imputation on rows of a matrix |
| jackknifeSE | Perform jackknife resampling on all columns of a... |
| lerp | Linear interpolation of a value |
| list_to_matrix | Convert a list of vectors to a binary matrix |
| map_value | Map a value in one range to a value in another |
| meta_de | Perform p-value combination for sets of differential... |
| minmax | Min-Max normalize a value within a given range |
| outliers_by_iqr | Compute outliers by IQR method |
| pairwise_fisher_test | Perform pairwise fisher.tests on an input matrix |
| pairwise_intersections | Get unique pairwise intersections of a list of vectors |
| panther_go | Perform GO analysis with PANTHER |
| permutation_correlation_test | Perform a permutation correlation test on every row of a... |
| permutations | Generate all permutations of a vector |
| plot_boxplot | Create boxplot from expression data |
| plot_cor_pairs | Plot pairwise correlations between columns of a matrix |
| plot_density | Density plot of expression values |
| plot_dist | Plot the distance between all columns of a matrix |
| plot_md | Create an MD plot from expression data |
| plot_parallel | Parallel coordinates plot of expression data |
| plot_umap | Plot results of UMAP |
| plot_volcano | Create a volcano plot from expression data |
| quickmap | Heatmap with sensible defaults for RNA-seq expression data |
| random_rgb_palette | Generate random RGB color palette |
| rank_threshold | Calculate threshold value on ranked input |
| rarefy | Rarefy (subsample) a matrix |
| read_bismark | Read in and Filter Bismark Coverage Files |
| remove_components | Remove principal components from data |
| remove_var | Remove low variance features from a matrix |
| sample_n_random_cor | Generate a null distribution of correlation values |
| simulate_counts | Generate simulated RNA-seq data for testing purposes |
| strip_ens | Strip version IDs from ENSEMBL identifiers |
| summarize_dge | Summarize RNA-seq expression results |
| theme_coriell | ggplot2 theme for coriell package |
| UMAP | Perform UMAP |
