InPAS                   A package for identifying novel Alternative
                        PolyAdenylation Sites (PAS) based on RNA-seq
                        data
UTR3eSet-class          UTR3eSet-class and its methods
assemble_allCov         Assemble coverage files for all samples
extract_UTR3Anno        extract 3' UTR information from a
                        GenomicFeatures::TxDb object
filter_testOut          filter 3' UTR usage test results
get_UTR3eSet            prepare 3' UTR coverage data for usage test
get_regionCov           Get coverage for 3' UTR and last CDS regions on
                        a single chromosome
get_ssRleCov            Get Rle coverage from a bedgraph file for a
                        sample
get_usage4plot          prepare coverage data and fitting data for plot
parse_TxDb              Extract gene models from a TxDb object
plot_utr3Usage          Visualize the dPDUI events using ggplot2
run_coverageQC          Quality control on read coverage over gene
                        bodies and 3UTRs
search_CPs              Estimate the CP sites for UTRs on a given
                        chromosome
setup_CPsSearch         prepare data for predicting cleavage and
                        polyadenylation (CP) sites
setup_GSEA              prepare files for GSEA analysis
setup_sqlitedb          Create an SQLite database for storing metadata
                        and paths to coverage files
test_dPDUI              do test for dPDUI
utr3.mm10               Annotation of 3' UTRs for mouse (mm10)
