ASE-methods             Use Limma, DESeq2 or DoubleExpSeq to test for
                        differential Alternative Splice Events
BuildReference          Builds reference files used by IRFinder /
                        NxtIRF.
CollateData             Processes data from IRFinder output
CoordToGR               Converts genomic coordinates into a GRanges
                        object
Coverage                Calls NxtIRF's C++ function to retrieve
                        coverage from a COV file
Find_Samples            Convenience Function to (recursively) find all
                        files in a folder.
IRFinder                Runs the OpenMP/C++-based NxtIRF/IRFinder
                        algorithm
IsCOV                   Validates the given file as a valid COV file
MakeSE                  Constructs a NxtSE object from the collated
                        data
Mappability-methods     Calculate low mappability genomic regions
NxtFilter-class         NxtIRF filters to remove low-abundance
                        alternative splicing and intron retention
                        events
NxtIRFcore-package      NxtIRFcore: a command line interface for NxtIRF
                        - IRFinder-based differential Alternative
                        Splicing and Intron Retention analysis
NxtSE-class             The NxtSE class
Plot_Coverage           RNA-seq Coverage Plots and Genome Tracks
Run_NxtIRF_Filters      Filtering for IR and Alternative Splicing
                        Events
STAR-methods            STAR wrapper for building reference for STAR,
                        and aligning RNA-sequencing
example-NxtIRF-data     NxtIRF Example BAMs and NxtSE Experiment Object
make_plot_data          Construct data of percent-spliced-in (PSI)
                        matrices and "diagonal" for heatmaps and
                        scatter plots
theme_white             ggplot2 themes
