Package index • phyloDS

Experiment Setup

Initialize and configure your analysis

newExperiment(): Initialize a phyloDS Experiment

OSJ Definition

Align orthologous sequences and count orthologous splice junctions

coverageSJ(): Count Splice Junction Coverage from BAM Files
orthogroupDNA(): Extract DNA Sequences for Orthogroups
orthogroupMSA(): Compute Multiple Sequence Alignments for Orthogroups
findOSJ(): Map Splice Junctions to Multiple Genomic Sequence Alignments

Normalization

Estimate size factors for count normalization

estSizeFactors(): Estimate Size Factors for Library Normalization

Differential Usage Testing and Simulation

Test for differential OSJ usage, and evaluate type I error control

runDS(): Test for Differential Splicing Between Groups
filterSignificantGenes(): Filter to Genes with Significant Orthologous Splice Junctions
runSimu(): Null Simulation Study for Differential Splicing Methods
plotSimu(): Plot Per-test Type I Error Rate from Null Simulations

Sequence-Level Validation

Predict splice site strength from genomic sequence alone

predictDID(): Predict Splice Site Strength Using OpenSpliceAI

Annotation and Export

Annotate and visualize differentially used OSJs

annotateOSJ(): Annotate Orthologous Splice Junctions with Flanking and Skipped Exons
exportResults(): Export phyloDS Results for IGV Visualization
showOSJ(): Display the Context of an Orthologous Splice Junction

Utilities

Helper functions

loadMSA(): Load Multiple Sequence Alignment with Coordinate Mapping