@article{Uhl_Rabsch_Eggenhofer-Peakh_indiv_site-2022,
author = {Uhl, Michael and Rabsch, Dominik and Eggenhofer, Florian 
          and Backofen, Rolf},
title = {Peakhood: individual site context extraction for {CLIP}-seq 
         peak regions},
journal = {Bioinformatics},
year = {2022},
doi = {10.1093/bioinformatics/btab755},
volume = {38},
user = {backofen},
pmid = {34734974},
pages = {1139-1140},
number = {4},
issn = {1367-4803},
abstract = {MOTIVATION: CLIP-seq is by far the most widely used method 
            to determine transcriptome-wide binding sites of RNA-binding 
            proteins (RBPs). The binding site locations are identified 
            from CLIP-seq read data by tools termed peak callers. Many 
            RBPs bind to a spliced RNA (i.e. transcript) context, but 
            all currently available peak callers only consider and 
            report the genomic context. To accurately model protein 
            binding behavior, a tool is needed for the individual 
            context assignment to CLIP-seq peak regions. RESULTS: Here 
            we present Peakhood, the first tool that utilizes CLIP-seq 
            peak regions identified by peak callers, in tandem with 
            CLIP-seq read information and genomic annotations, to 
            determine which context applies, individually for each peak 
            region. For sites assigned to transcript context, it further 
            determines the most likely splice variant, and merges 
            results for any number of datasets to obtain a comprehensive 
            collection of transcript context binding sites. AVAILABILITY 
            AND IMPLEMENTATION: Peakhood is freely available under MIT 
            license at: https://github.com/BackofenLab/Peakhood. 
            SUPPLEMENTARY INFORMATION: Supplementary data are available 
            at Bioinformatics online.}
}