ASE-GLM-edgeR           Using Generalised linear models (GLMs) to
                        analyse differential ASEs using edgeR
ASE-methods             Differential Alternative Splicing Event
                        analysis
ASEFilter-class         SpliceWiz filters to remove low-confidence
                        alternative splicing and intron retention
                        events
Build-Reference-methods
                        Builds reference files used by SpliceWiz
Coverage                Calls SpliceWiz's C++ function to retrieve
                        coverage from a COV file
Gene-ontology-methods   Gene ontology (over-representation) analysis
                        using enriched genes of top alternative
                        splicing events
Graphics-User-Interface
                        Launches the SpliceWiz Graphics User Interface
                        (GUI) using Shiny Dashboard
Mappability-methods     Calculate low mappability genomic regions
NxtSE-class             The NxtSE class
Run_SpliceWiz_Filters   Filtering for IR and Alternative Splicing
                        Events
STAR-methods            STAR wrappers for building reference for STAR,
                        and aligning RNA-sequencing
SpliceWiz-package       SpliceWiz: efficient and precise alternative
                        splicing analysis in R
View-Reference-methods
                        View SpliceWiz Reference in read-able data
                        frames
collateData             Collates a dataset from (processBAM) output
                        files of individual samples
coord2GR                Converts genomic coordinates into a GRanges
                        object
covDataObject-class     Container to hold raw data for SpliceWiz
                        coverage plots
covPlotObject-class     Versatile coverage plots for SpliceWiz
covPlotly-class         Container for plotly-based coverage plots
example-SpliceWiz-data
                        SpliceWiz Example BAMs and NxtSE Experiment
                        Object
findSamples             Convenience Function to (recursively) find all
                        files in a folder.
isCOV                   Validates the given file as a valid COV file
makeSE                  Imports a collated dataset into the R session
                        as an NxtSE object
make_plot_data          Construct data of percent-spliced-in (PSI)
                        matrices and group-average PSIs
plotCoverage            RNA-seq Coverage Plots and Genome Tracks
processBAM              Runs the OpenMP/C++ based SpliceWiz algorithm
setSWthreads            Sets the number of threads used by SpliceWiz
theme_white             ggplot2 themes
