Package index • coriell

All functions

GSE161650_de: Differential expression results from GSE161650

GSE161650_lc: Normalized log2 counts from GSE161650

UMAP(): Perform UMAP

associate_components(): Calculate associations between variables and principal components

clamp(): Limit values to a given range

clr(): Centered Log-ratio transformation

colmean(): Give means of rows of matrix based on column grouping variable

dfs2se(): Convert a list of differential expression data.frames to a SummarizedExperiment

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 environment

geometric_mean(): Geometric mean of a vector

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 SummarizeExperiment object

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 expression tests

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 matrix

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