Metadensity: a background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites.
Metadensity: a background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites.
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DOI：
10.1093/bioadv/vbac083
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发表时间：
2022
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Cross-linking and immunoprecipitation (CLIP) is a technology to map the binding sites of RNA-binding proteins (RBPs). The region where an RBP binds within RNA is often indicative of its molecular function in RNA processing. As an example, the binding sites of splicing factors are found within or proximal to alternatively spliced exons. To better reveal the function of RBPs, we developed a tool to visualize the distribution of CLIP signals around various transcript features. Here, we present Metadensity (https://github.com/YeoLab/Metadensity), a software that allows users to generate metagene plots. Metadensity allows users to input features such as branchpoints and preserves the near-nucleotide resolution of CLIP technologies by not scaling the features by length. Metadensity normalizes immunoprecipitated libraries with background controls, such as size-matched inputs, then windowing in various user-defined features. Finally, the signals are averaged across a provided set of transcripts. Metadensity is available at https://github.com/YeoLab/Metadensity, with example notebooks at https://metadensity.readthedocs.io/en/latest/tutorial.html. Supplementary data are available at Bioinformatics Advances online.
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影响因子：
64.5
作者：
Hafner M;Landthaler M;Burger L;Khorshid M;Hausser J;Berninger P;Rothballer A;Ascano M Jr;Jungkamp AC;Munschauer M;Ulrich A;Wardle GS;Dewell S;Zavolan M;Tuschl T
通讯作者：
Tuschl T
影响因子：
48
作者：
Van Nostrand EL;Pratt GA;Shishkin AA;Gelboin-Burkhart C;Fang MY;Sundararaman B;Blue SM;Nguyen TB;Surka C;Elkins K;Stanton R;Rigo F;Guttman M;Yeo GW
通讯作者：
Yeo GW
影响因子：
64.8
作者：
MOORE, MJ;SHARP, PA
通讯作者：
SHARP, PA
影响因子：
16.8
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影响因子：
16.8
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