{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T21:23:22Z","timestamp":1773350602332,"version":"3.50.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"3","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000069","name":"National Institute of Arthritis and Musculoskeletal and Skin Diseases","doi-asserted-by":"publisher","award":["ZIA-AR041205"],"award-info":[{"award-number":["ZIA-AR041205"]}],"id":[{"id":"10.13039\/100000069","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>PAR-CLIP is a widely used method for identifying binding sites of RNA-binding proteins (RBPs) transcriptome-wide. A characteristic T-to-C transition in the sequenced complementary DNA pinpoints the site of RBP-RNA crosslinking and is induced by the use of a photoreactive uridine analogue, 4-thiouridine (4SU). As with other system-wide methods, PAR-CLIP, too, is prone to false discoveries, as the T-to-C signal might result from systematic noise, pre-existing SNPs, and polymerase chain reaction errors. Therefore, rigorous statistical methods are required for analyzing PAR-CLIP data. The few existing tools to analyze PAR-CLIP data lack updates and sufficient documentation, and often fail to process current higher-depth sequencing data. Here, we report PCLIPtools, a lightweight, customizable suite for analyzing PAR-CLIP data. PCLIPtools considers the read depth, T-to-C transitions, and the other mutations to statistically estimate high-confidence interaction sites. Benchmarking shows that PCLIPtools identifies more functionally significant targets than the current standard tool, PARalyzer, without losing high-confidence sites and outperforming it in runtime. Exploratory analyses show PCLIPtools\u2019 specific targets are enriched for read depth and T-to-C conversion, supporting their validity. With simplicity, robustness, and speed, PCLIPtools improves the precision of PAR-CLIP data analysis while being accessible to experimental RNA biologists.<\/jats:p>","DOI":"10.1093\/nar\/gkag062","type":"journal-article","created":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T12:42:57Z","timestamp":1768999377000},"source":"Crossref","is-referenced-by-count":1,"title":["PCLIPtools: a robust framework for identifying RNA-protein interaction sites from PAR-CLIP experiments"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6591-3164","authenticated-orcid":false,"given":"Ahsan H","family":"Polash","sequence":"first","affiliation":[{"name":"RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health (NIH) , Bethesda, MD 20892 ,","place":["United 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