allauc                  Calculate Area Under Curve (AUC) and
                        Differences of AUC for Transcript Data
attenuation             Calculate Attenuation from AUC and Other
                        Transcript Features
averageandfilterexprs   Calculate Average Expression and Filter
                        Transcript Data
blacklisthighmap        Blacklist High Mappability Regions in Genomic
                        Data
checkexptab             Check Validity of Experiment Table
countna                 Count NA values per transcript and condition
createtablescores       Create a Unified Table of Scores
genesECDF               Compute ECDF for Genes Based on Expression Data
kneeallconds            Calculate knee for each condition separately
kneeid                  Identify the Knee and Max ECDF Differences for
                        Each Transcript
makewindows             Split Gene Annotations into Fixed-Size Windows
meandifference          Compute Mean and Differences of Scores for Each
                        Condition
plotauc                 Plot AUC Comparison Between Conditions
plotecdf                Plot Empirical Cumulative Distribution Function
                        (ECDF)
plothistoknee           Plot Histogram of Distance from TSS to Knee
                        Point
plotmetagenes           Plot Metagenes for Gene Groups
plotmulti               Generate all tepr plots for all experiment
                        comparisons
preprocessing           Preprocess Experimental Data for Genomic
                        Analysis
retrieveanno            Retrieve and Combine Annotation Information
retrievechrom           Retrieve chromosome lengths and information for
                        a specified genome.
showallcomp             Retrieve all the comparison names from the
                        experiment table
tepr                    Perform the tepr differential nascent rna-seq
                        analysis
teprmulti               Perform tepr differential nascent rna-seq
                        analysis for multiple conditions
universegroup           Define Universe and Group of Genes Based on
                        Expression Data
