# interactive analysis and visualization of alternative splicing in R

## Documentation for package ‘SpliceWiz’ version 1.13.0

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

## Help Pages

A B C D E F G I J M N P R S T U V misc

SpliceWiz-package | SpliceWiz: efficient and precise alternative splicing analysis in R

## -- A --

addPSI_edgeR | Using Generalised linear models (GLMs) to analyse differential ASEs using edgeR
applyFilters | Filtering for IR and Alternative Splicing Events
ASE-GLM-edgeR | Using Generalised linear models (GLMs) to analyse differential ASEs using edgeR
ASE-methods | Differential Alternative Splicing Event analysis
ASEFilter | SpliceWiz filters to remove low-confidence alternative splicing and intron retention events
ASEFilter-class | SpliceWiz filters to remove low-confidence alternative splicing and intron retention events
ASE_DESeq | Differential Alternative Splicing Event analysis
ASE_DoubleExpSeq | Differential Alternative Splicing Event analysis
ASE_edgeR | Differential Alternative Splicing Event analysis
ASE_edgeR_timeseries | Differential Alternative Splicing Event analysis
ASE_limma | Differential Alternative Splicing Event analysis
ASE_limma_timeseries | Differential Alternative Splicing Event analysis

## -- B --

BAM2COV | Runs the OpenMP/C++ based SpliceWiz algorithm
Build-Reference-methods | Builds reference files used by SpliceWiz
buildFullRef | Builds reference files used by SpliceWiz
buildRef | Builds reference files used by SpliceWiz

## -- C --

calculateMappability | Calculate low mappability genomic regions
cbind-method | The NxtSE class
coerce-method | The NxtSE class
collateData | Collates a dataset from (processBAM) output files of individual samples
condition | Versatile coverage plots for SpliceWiz
condition-method | Versatile coverage plots for SpliceWiz
coord2GR | Converts genomic coordinates into a GRanges object
covDataObject-class | Container to hold raw data for SpliceWiz coverage plots
Coverage | Calls SpliceWiz's C++ function to retrieve coverage from a COV file
covfile | The NxtSE class
covfile-method | The NxtSE class
covfile<- | The NxtSE class
covfile<--method | The NxtSE class
covPlotly-class | Container for plotly-based coverage plots
covPlotObject-class | Versatile coverage plots for SpliceWiz

## -- D --

down_exc | The NxtSE class
down_exc-method | The NxtSE class
down_exc<- | The NxtSE class
down_exc<--method | The NxtSE class
down_inc | The NxtSE class
down_inc-method | The NxtSE class
down_inc<- | The NxtSE class
down_inc<--method | The NxtSE class

## -- E --

example-SpliceWiz-data | SpliceWiz Example BAMs and NxtSE Experiment Object
extract_gene_ids_for_GO | Gene ontology (over-representation) analysis using enriched genes of top alternative splicing events

## -- F --

findBAMS | Convenience Function to (recursively) find all files in a folder.
findFASTQ | Convenience Function to (recursively) find all files in a folder.
findSamples | Convenience Function to (recursively) find all files in a folder.
findSpliceWizOutput | Convenience Function to (recursively) find all files in a folder.
fitASE_edgeR | Using Generalised linear models (GLMs) to analyse differential ASEs using edgeR
fitASE_edgeR_custom | Using Generalised linear models (GLMs) to analyse differential ASEs using edgeR

## -- G --

Gene-ontology-methods | Gene ontology (over-representation) analysis using enriched genes of top alternative splicing events
generateSyntheticReads | Calculate low mappability genomic regions
getAvailableGO | Builds reference files used by SpliceWiz
getCoverage | Calls SpliceWiz's C++ function to retrieve coverage from a COV file
getCoverageBins | Calls SpliceWiz's C++ function to retrieve coverage from a COV file
getCoverageData | Container to hold raw data for SpliceWiz coverage plots
getCoverageRegions | Calls SpliceWiz's C++ function to retrieve coverage from a COV file
getCoverage_DF | Calls SpliceWiz's C++ function to retrieve coverage from a COV file
getDefaultFilters | Filtering for IR and Alternative Splicing Events
getExonRanges | Container for plotly-based coverage plots
getExonRanges-method | Container for plotly-based coverage plots
getGenomeData | Container to hold raw data for SpliceWiz coverage plots
getNonPolyARef | Builds reference files used by SpliceWiz
getPlotObject | Versatile coverage plots for SpliceWiz
getResources | Builds reference files used by SpliceWiz
goASE | Gene ontology (over-representation) analysis using enriched genes of top alternative splicing events
goGenes | 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
GUI | Launches the SpliceWiz Graphics User Interface (GUI) using Shiny Dashboard

## -- I --

isCOV | Validates the given file as a valid COV file

## -- J --

junc_counts | The NxtSE class
junc_counts-method | The NxtSE class
junc_counts_uns | The NxtSE class
junc_counts_uns-method | The NxtSE class
junc_gr | The NxtSE class
junc_gr-method | The NxtSE class
junc_PSI | The NxtSE class
junc_PSI-method | The NxtSE class

## -- M --

makeMatrix | Construct data of percent-spliced-in (PSI) matrices and group-average PSIs
makeMeanPSI | Construct data of percent-spliced-in (PSI) matrices and group-average PSIs
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
Mappability-methods | Calculate low mappability genomic regions

## -- N --

NxtSE | The NxtSE class
NxtSE-class | The NxtSE class
NxtSE-methods | The NxtSE class

## -- P --

plotAnnoTrack | Container to hold raw data for SpliceWiz coverage plots
plotCoverage | RNA-seq Coverage Plots and Genome Tracks
plotGenome | RNA-seq Coverage Plots and Genome Tracks
plotGO | Gene ontology (over-representation) analysis using enriched genes of top alternative splicing events
plotView | Versatile coverage plots for SpliceWiz
processBAM | Runs the OpenMP/C++ based SpliceWiz algorithm

## -- R --

rbind-method | The NxtSE class
realize_NxtSE | The NxtSE class
realize_NxtSE-method | The NxtSE class
ref | The NxtSE class
ref-method | The NxtSE class
row_gr | The NxtSE class
row_gr-method | The NxtSE class
runFilter | Filtering for IR and Alternative Splicing Events
Run_SpliceWiz_Filters | Filtering for IR and Alternative Splicing Events

## -- S --

sampleQC | The NxtSE class
sampleQC-method | The NxtSE class
sampleQC<- | The NxtSE class
sampleQC<--method | The NxtSE class
setResolution | Container for plotly-based coverage plots
setResolution-method | Container for plotly-based coverage plots
setSWthreads | Sets the number of threads used by SpliceWiz
showEvents | Container to hold raw data for SpliceWiz coverage plots
showEvents-method | Container to hold raw data for SpliceWiz coverage plots
showExons | Container for plotly-based coverage plots
showExons-method | Container for plotly-based coverage plots
sourcePath | The NxtSE class
sourcePath-method | The NxtSE class
SpliceWiz | SpliceWiz: efficient and precise alternative splicing analysis in R
spliceWiz | Launches the SpliceWiz Graphics User Interface (GUI) using Shiny Dashboard
SpliceWiz_example_bams | SpliceWiz Example BAMs and NxtSE Experiment Object
SpliceWiz_example_NxtSE | SpliceWiz Example BAMs and NxtSE Experiment Object
STAR-methods | STAR wrappers for building reference for STAR, and aligning RNA-sequencing
STAR_alignExperiment | STAR wrappers for building reference for STAR, and aligning RNA-sequencing
STAR_alignReads | STAR wrappers for building reference for STAR, and aligning RNA-sequencing
STAR_buildGenome | STAR wrappers for building reference for STAR, and aligning RNA-sequencing
STAR_buildRef | STAR wrappers for building reference for STAR, and aligning RNA-sequencing
STAR_loadGenomeGTF | STAR wrappers for building reference for STAR, and aligning RNA-sequencing
STAR_mappability | STAR wrappers for building reference for STAR, and aligning RNA-sequencing
STAR_version | STAR wrappers for building reference for STAR, and aligning RNA-sequencing
subset_EventNames_by_GO | Gene ontology (over-representation) analysis using enriched genes of top alternative splicing events

## -- T --

testASE_edgeR | Using Generalised linear models (GLMs) to analyse differential ASEs using edgeR
theme_white | ggplot2 themes
theme_white_legend | ggplot2 themes
theme_white_legend_plot_track | ggplot2 themes
tracks | Versatile coverage plots for SpliceWiz
tracks-method | Versatile coverage plots for SpliceWiz

## -- U --

update_NxtSE | The NxtSE class
update_NxtSE-method | The NxtSE class
up_exc | The NxtSE class
up_exc-method | The NxtSE class
up_exc<- | The NxtSE class
up_exc<--method | The NxtSE class
up_inc | The NxtSE class
up_inc-method | The NxtSE class
up_inc<- | The NxtSE class
up_inc<--method | The NxtSE class

## -- V --

View-Reference-methods | View SpliceWiz Reference in read-able data frames
viewASE | View SpliceWiz Reference in read-able data frames
viewExons | View SpliceWiz Reference in read-able data frames
viewGenes | View SpliceWiz Reference in read-able data frames
viewGO | View SpliceWiz Reference in read-able data frames
viewIntrons | View SpliceWiz Reference in read-able data frames
viewIR | View SpliceWiz Reference in read-able data frames
viewIR_NMD | View SpliceWiz Reference in read-able data frames
viewProteins | View SpliceWiz Reference in read-able data frames
viewTranscripts | View SpliceWiz Reference in read-able data frames

## -- misc --

[-method | The NxtSE class
[<--method | The NxtSE class