Easy, optimized, and accurate alternative splicing analysis in R

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Documentation for package ‘SpliceWiz’ version 1.2.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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 to analyse differential ASEs using edgeR
applyFilters	Filtering for IR and Alternative Splicing Events
ASE-GLM-edgeR	Using Generalised linear models 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 to analyse differential ASEs using edgeR
fitASE_edgeR_custom	Using Generalised linear models 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	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 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