ArticleBMC research notes2018
Empowering the detection of ChIP-seq "basic peaks" (bPeaks) in small eukaryotic genomes with a web user-interactive interface.
Article in BMC research notes, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
3 citing papers in PubMed.
- ChIP-SICAP: A New Tool to Explore Gene-Regulatory Networks in Candida albicans and Other Yeasts.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Omics Analyses: How to Navigate Through a Constant Data Deluge.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Yap5 Competes With Hap4 for the Regulation of Iron Homeostasis Genes in the Human PathogenFrontiers in cellular and infection microbiology · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
objectivebPeaks is a peak calling program to detect protein DNA-binding sites from ChIPseq data in small eukaryotic genomes. The simplicity of the bPeaks method is well appreciated by users, but its use via an R package is challenging and time-consuming for people without programming skills. In addition, user feedback has highlighted the lack of a convenient way to carefully explore bPeaks result files. In this context, the development of a web user interface represents an important added value for expanding the bPeaks user community.
resultsWe developed a new bPeaks application (bPeaks App). The application allows the user to perform all the peak-calling analysis steps with bPeaks in a few mouse clicks via a web browser. We added new features relative to the original R package, particularly the possibility to import personal annotation files to compare the location of the detected peaks with specific genomic elements of interest of the user, in any organism, and a new organization of the result files which are directly manageable via a user-interactive genome browser. This significantly improves the ability of the user to explore all detected basic peaks in detail.
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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.