Transcription Elongation Profiling

Documentation for package ‘tepr’ version 1.1.8

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
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