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(): Flag outliers by IQR
outliers_by_mad(): Flag outliers by MAD
outliers_by_z(): Flag outliers by z-score
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_beads(): Create a methylation bead plot
plot_boxplot(): Create boxplot from expression data
plot_boxplot2(): Show boxplots for columns of data in a matrix
plot_cor_pairs(): Plot pairwise correlations between columns of a matrix
plot_density(): Density plot of expression values
plot_density2(): Create a density plot from the columns of a matrix
plot_dist(): Plot the distance between all columns of a matrix
plot_enrichment(): GSEA enrichment plot
plot_md(): Create an MD plot from expression data
plot_meth_hist(): Create a binned histogram of methylation percentage statistics
plot_parallel(): Parallel coordinates plot of expression data
plot_parallel2(): Parallel coordinates plot
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
setup_chunk(): Setup Chunk Generator
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
tpm(): Compute TPM normalized counts