| 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 |