Man pages for alexchwong/NxtIRFcore
Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine
| ASE-methods | Use Limma, DESeq2 or DoubleExpSeq to test for differential... |
| BuildReference | Builds reference files used by IRFinder / NxtIRF. |
| 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... |
| example-NxtIRF-data | NxtIRF Example BAMs and NxtSE Experiment Object |
| Find_Samples | Convenience Function to (recursively) find all files in a... |
| IRFinder | Runs the OpenMP/C++-based NxtIRF/IRFinder algorithm |
| IsCOV | Validates the given file as a valid COV file |
| make_plot_data | Construct data of percent-spliced-in (PSI) matrices and... |
| MakeSE | Constructs a NxtSE object from the collated data |
| Mappability-methods | Calculate low mappability genomic regions |
| NxtFilter-class | NxtIRF filters to remove low-abundance alternative splicing... |
| NxtIRFcore-package | NxtIRFcore: a command line interface for NxtIRF -... |
| NxtSE-class | The NxtSE class |
| Plot_Coverage | RNA-seq Coverage Plots and Genome Tracks |
| Run_NxtIRF_Filters | Filtering for IR and Alternative Splicing Events |
| STAR-methods | STAR wrapper for building reference for STAR, and aligning... |
| theme_white | ggplot2 themes |
