# Transcription Elongation Profiling

## Documentation for package ‘tepr’ version 1.1.15

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

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