InPAS                   A package for identifying novel Alternative
                        PolyAdenylation Sites (PAS) based on RNA-seq
                        data
UTR3eSet-class          UTR3eSet-class and its methods
addChr2Exclude          Add a globally-applied requirement for
                        filtering out scaffolds from all analysis
addInPASEnsDb           Add a globally defined EnsDb to some InPAS
                        functions.
addInPASGenome          Add a globally defined genome to all InPAS
                        functions.
addInPASOutputDirectory
                        Add a globally defined output directory to some
                        InPAS functions.
addInPASTxDb            Add a globally defined TxDb for InPAS
                        functions.
addLockName             Add a filename for locking a SQLite database
assemble_allCov         Assemble coverage files for a given chromosome
                        for all samples
extract_UTR3Anno        extract 3' UTR information from a
                        GenomicFeatures::TxDb object
filter_testOut          filter 3' UTR usage test results
find_minMSEDistr        Visualization of MSE profiles, 3' UTR coverage
                        and minimal MSE distribution
getChr2Exclude          Get a globally-applied requirement for
                        filtering scaffolds.
getInPASEnsDb           Get the globally defined EnsDb.
getInPASGenome          Get the globally defined genome
getInPASOutputDirectory
                        Get the path to a output directory for InPAS
                        analysis
getInPASSQLiteDb        Get the path to an SQLite database
getInPASTxDb            Get the globally defined TxDb.
getLockName             Get the path to a file for locking the SQLite
                        database
get_UTR3eSet            prepare 3' UTR coverage data for usage test
get_chromosomes         Identify chromosomes/scaffolds for CP site
                        discovery
get_lastCDSUTR3         Extract the last unspliced region of each
                        transcript
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
set_globals             Set up global variables for an InPAS analysis
setup_CPsSearch         prepare data for predicting cleavage and
                        polyadenylation (CP) sites
setup_GSEA              prepare files for GSEA analysis
setup_parCPsSearch      Prepare data for predicting cleavage and
                        polyadenylation (CP) sites using parallel
                        computing
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)
