ArticleBioinformatics advances2022
Metadensity: a background-aware python pipeline for summarizing CLIP signals on various transcriptomic sites.
Article in Bioinformatics advances, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 10 citations in OpenAlex.
- Integrative CRISPR Screening and RNA Analyses Discover an Essential Role for PUF60 Interactions with 3' Splice Sites in Cancer Progression.Cancer research · 2026Article
- Flipper: An advanced framework for identifying differential RNA binding behavior with eCLIP data.bioRxiv : the preprint server for biology · 2026Article
- Article
- Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation.Molecular cell · 2024Article
- Large-scale map of RNA-binding protein interactomes across the mRNA life cycle.Molecular cell · 2024Article
- MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots.BMC bioinformatics · 2024Article
- Remodeling oncogenic transcriptomes by small molecules targeting NONO.Nature chemical biology · 2023Article
- Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.Cell genomics · 2023Article
- Large-scale map of RNA binding protein interactomes across the mRNA life-cycle.bioRxiv : the preprint server for biology · 2023Article
- Proteomic discovery of chemical probes that perturb protein complexes in human cells.Molecular cell · 2023Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Motivation: 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. Results: 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. Availability and implementation: Metadensity is available at https://github.com/YeoLab/Metadensity, with example notebooks at https://metadensity.readthedocs.io/en/latest/tutorial.html. Supplementary information: Supplementary data are available at
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.