Advances in high-throughput profiling of RNA-binding proteins (RBPs) have resulted in CLIP-seq datasets coupled with transcriptome profiling by RNA-seq. However, analysis methods that integrate both types of data are lacking. We describe SURF, Statistical Utility for RBP Functions, for integrative analysis of large collections of CLIP-seq and RNA-seq data to identify alternative splicing (AS), alternative transcription initiation (ATI), and alternative polyadenylation (APA) events regulated by individual RBPs and elucidate protein-RNA interactions governing these events.
|Bioconductor views||Alignment AlternativeSplicing Coverage DNASeq DataImport RNASeq Sequencing Transcription Visualization|
|Package repository||View on GitHub|
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