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


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Documentation for package ‘NxtIRFcore’ version 1.4.0

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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