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 |