Man pages for alexchwong/SpliceWiz
interactive analysis and visualization of alternative splicing in R
| ASEFilter-class | SpliceWiz filters to remove low-confidence alternative... |
| ASE-GLM-edgeR | Using Generalised linear models (GLMs) to analyse... |
| ASE-methods | Differential Alternative Splicing Event analysis |
| Build-Reference-methods | Builds reference files used by SpliceWiz |
| collateData | Collates a dataset from (processBAM) output files of... |
| coord2GR | Converts genomic coordinates into a GRanges object |
| covDataObject-class | Container to hold raw data for SpliceWiz coverage plots |
| Coverage | Calls SpliceWiz's C++ function to retrieve coverage from a... |
| covPlotly-class | Container for plotly-based coverage plots |
| covPlotObject-class | Versatile coverage plots for SpliceWiz |
| example-SpliceWiz-data | SpliceWiz Example BAMs and NxtSE Experiment Object |
| findSamples | Convenience Function to (recursively) find all files in a... |
| Gene-ontology-methods | Gene ontology (over-representation) analysis using enriched... |
| Graphics-User-Interface | Launches the SpliceWiz Graphics User Interface (GUI) using... |
| isCOV | Validates the given file as a valid COV file |
| make_plot_data | Construct data of percent-spliced-in (PSI) matrices and... |
| makeSE | Imports a collated dataset into the R session as an NxtSE... |
| Mappability-methods | Calculate low mappability genomic regions |
| NxtSE-class | The NxtSE class |
| plotCoverage | RNA-seq Coverage Plots and Genome Tracks |
| processBAM | Runs the OpenMP/C++ based SpliceWiz algorithm |
| Run_SpliceWiz_Filters | Filtering for IR and Alternative Splicing Events |
| setSWthreads | Sets the number of threads used by SpliceWiz |
| SpliceWiz-package | SpliceWiz: efficient and precise alternative splicing... |
| STAR-methods | STAR wrappers for building reference for STAR, and aligning... |
| theme_white | ggplot2 themes |
| View-Reference-methods | View SpliceWiz Reference in read-able data frames |
