Package index

Visualization

Core functions for producing peak visualizations on gene and genomic region structures.

PlotGene()

Plot RNA-Binding Protein Peaks on a Single Gene

PlotRegion()

Plot RNA-Binding Protein Peaks on a Genomic Region

Splicing and Motif Analysis

Functions for quantifying RNA-binding protein occupancy and sequence motif frequency around exon-intron boundaries.

createSplicingMap()

Create Splicing Map

createRetainedIntronSplicingMap()

Create Retained Intron Splicing Map

createSequenceMap()

Create Sequence Map Analyzes the frequency of a target sequence motif across splicing junction regions. Compares motif frequency between Retained, Excluded, and Control splicing events to identify position-specific enrichment patterns.

createRetainedIntronSequenceMap()

Create Retained Intron Sequence Map

Utilities

Helper functions for loading annotations and preparing input data.

LoadGTF()

Can be called once and the result passed to PlotGene() or PlotRegion() to avoid repeated downloads.

checkBed()

Validate and Normalize a BED-Format Data Frame

Sample Data

Curated datasets bundled with the package for testing and demonstration.

sample_bed

Sample K562 RBP Binding Peaks

sample_se.mats

Sample SE.MATS Skipped-Exon Splicing Events

gtf_human

Human GTF Gene Annotation

Package

Package-level documentation.

RNAPeaks RNAPeaks-package

RNAPeaks: Visualize RNA-Binding Protein Peaks on Gene Structures