Package index • SplineOmics

User Available Functions

This section contains the documentation for all functions available to the user in the SplineOmics package.

compare_results(): Compare hits between two SplineOmics results

cluster_hits(): Cluster the significant features based on spline similarity

create_limma_report(): Generate HTML report with p-value histograms of all the features

create_splineomics(): Create an object containing variables often used by SplineOmics functions

extract_gene_sets(): Download gene set annotations from Bioconductor organism databases

download_enrichr_databases(): Download the Enrichr databases

explore_data(): Automatically perform exploratory data analysis (EDA)

extract_data(): Extract a rectangular block from a dataframe and make it to a matrix

find_pvc(): Find peaks and valleys in time-series omics data

preprocess_rna_seq_data(): Perform essential preprocessing steps for raw RNA-seq counts

print(<SplineOmics>): Print function for SplineOmics objects

run_ora(): Perform over-representation analysis with the results from cluster_hits()

run_limma_splines(): Perform a limma spline analysis to identify significant features

update_splineomics(): Update the variables in a SplineOmics object