ArticleBioinformatics (Oxford, England)2023
htseq-clip: a toolset for the preprocessing of eCLIP/iCLIP datasets.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- RNA-coupled CRISPR screens reveal ZNF207 as a regulator of LMNA aberrant splicing in progeria.Molecular cell · 2026Article
- LncRNA-Protein Interactions: A Key to Deciphering LncRNA Mechanisms.Biomolecules · 2025Review
- Article
- RNA helicase D1PAS1 resolves R-loops and forms a complex for mouse pachytene piRNA biogenesis required for male fertility.Nucleic acids research · 2024Article
- Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq.Nucleic acids research · 2024Article
- Characterization of RVFV Nucleocapsid Protein Binding Sites on RNA by iCLIP-seq.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Efficient and sensitive profiling of RNA-protein interactions using TLC-CLIP.Nucleic acids research · 2023Article
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Authors and funding
7 authors.
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Abstract
summaryTranscriptome-wide detection of binding sites of RNA-binding proteins is achieved using Individual-nucleotide crosslinking and immunoprecipitation (iCLIP) and its derivative enhanced CLIP (eCLIP) sequencing methods. Here, we introduce htseq-clip, a python package developed for preprocessing, extracting and summarizing crosslink site counts from i/eCLIP experimental data. The package delivers crosslink site count matrices along with other metrics, which can be directly used for filtering and downstream analyses such as the identification of differential binding sites. AVAILABILITY AND IMPLEMENTATION: The Python package htseq-clip is available via pypi (python package index), bioconda and the Galaxy Tool Shed under the open source MIT License. The code is hosted at https://github.com/EMBL-Hentze-group/htseq-clip and documentation is available under https://htseq-clip.readthedocs.io/en/latest.
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