# Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine

## Documentation for package ‘NxtIRFcore’ version 1.6.0

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

## Help Pages

NxtIRFcore-package | NxtIRFcore: a command line interface for NxtIRF - IRFinder-based differential Alternative Splicing and Intron Retention analysis
apply_filters | Filtering for IR and Alternative Splicing Events
ASE-methods | Use Limma, DESeq2 or DoubleExpSeq to test for differential Alternative Splice Events
as_egg_ggplot | RNA-seq Coverage Plots and Genome Tracks
BAM2COV | Runs the OpenMP/C++-based NxtIRF/IRFinder algorithm
BuildReference | Builds reference files used by IRFinder / NxtIRF.
BuildReference_Full | Builds reference files used by IRFinder / NxtIRF.
cbind-method | The NxtSE class
coerce-method | The NxtSE class
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
covfile | The NxtSE class
covfile-method | The NxtSE class
covfile<- | The NxtSE class
covfile<--method | The NxtSE class
DESeq_ASE | Use Limma, DESeq2 or DoubleExpSeq to test for differential Alternative Splice Events
DoubleExpSeq_ASE | Use Limma, DESeq2 or DoubleExpSeq to test for differential Alternative Splice Events
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
example-NxtIRF-data | NxtIRF Example BAMs and NxtSE Experiment Object
Find_Bams | Convenience Function to (recursively) find all files in a folder.
Find_FASTQ | Convenience Function to (recursively) find all files in a folder.
Find_IRFinder_Output | Convenience Function to (recursively) find all files in a folder.
Find_Samples | Convenience Function to (recursively) find all files in a folder.
GetCoverage | Calls NxtIRF's C++ function to retrieve coverage from a COV file
GetCoverageBins | Calls NxtIRF's C++ function to retrieve coverage from a COV file
GetCoverageRegions | Calls NxtIRF's C++ function to retrieve coverage from a COV file
GetCoverage_DF | Calls NxtIRF's C++ function to retrieve coverage from a COV file
GetNonPolyARef | Builds reference files used by IRFinder / NxtIRF.
GetReferenceResource | Builds reference files used by IRFinder / NxtIRF.
get_default_filters | Filtering for IR and Alternative Splicing Events
IRFinder | Runs the OpenMP/C++-based NxtIRF/IRFinder algorithm
IsCOV | Validates the given file as a valid COV file
limma_ASE | Use Limma, DESeq2 or DoubleExpSeq to test for differential Alternative Splice Events
MakeSE | Constructs a NxtSE object from the collated data
make_diagonal | Construct data of percent-spliced-in (PSI) matrices and "diagonal" for heatmaps and scatter plots
make_matrix | Construct data of percent-spliced-in (PSI) matrices and "diagonal" for heatmaps and scatter plots
make_plot_data | Construct data of percent-spliced-in (PSI) matrices and "diagonal" for heatmaps and scatter plots
Mappability-methods | Calculate low mappability genomic regions
Mappability_CalculateExclusions | Calculate low mappability genomic regions
Mappability_GenReads | Calculate low mappability genomic regions
NxtFilter | NxtIRF filters to remove low-abundance alternative splicing and intron retention events
NxtFilter-class | NxtIRF filters to remove low-abundance alternative splicing and intron retention events
NxtIRF_example_bams | NxtIRF Example BAMs and NxtSE Experiment Object
NxtIRF_example_NxtSE | NxtIRF Example BAMs and NxtSE Experiment Object
NxtSE | The NxtSE class
NxtSE-class | The NxtSE class
NxtSE-methods | The NxtSE class
Plot_Coverage | RNA-seq Coverage Plots and Genome Tracks
Plot_Genome | RNA-seq Coverage Plots and Genome Tracks
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
runFilter | Filtering for IR and Alternative Splicing Events
Run_NxtIRF_Filters | Filtering for IR and Alternative Splicing Events
sampleQC | The NxtSE class
sampleQC-method | The NxtSE class
sampleQC<- | The NxtSE class
sampleQC<--method | The NxtSE class
STAR-methods | STAR wrapper for building reference for STAR, and aligning RNA-sequencing
STAR_align_experiment | STAR wrapper for building reference for STAR, and aligning RNA-sequencing
STAR_align_fastq | STAR wrapper for building reference for STAR, and aligning RNA-sequencing
STAR_buildRef | STAR wrapper for building reference for STAR, and aligning RNA-sequencing
STAR_Mappability | STAR wrapper for building reference for STAR, and aligning RNA-sequencing
STAR_version | STAR wrapper for building reference for STAR, and aligning RNA-sequencing
theme_white | ggplot2 themes
theme_white_legend | ggplot2 themes
theme_white_legend_plot_track | ggplot2 themes
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
[-method | The NxtSE class
[<--method | The NxtSE class