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Today, I will talk to you about how to understand annoPeakR, an online tool for peak comments, which may not be understood by many people. In order to make you understand better, the editor has summarized the following for you. I hope you can get something according to this article.

AnnoPeakR is a peak annotation tool based on the shiny package in R language to develop web applications.

Multiple versions of human and mouse reference genome information are integrated. You only need to upload peak files in bed format for analysis. You can upload more than one at a time, as shown below.

Test data are also available on the official website, which can be seen by clicking Load sample Data. For the Peak file, only four columns are required, representing the chromosome, the start, the termination position, and the name of the peak, as shown below

For each peak file, the following two types of comment information are provided

1. Peak associated gene structures

The analysis of peak associated genes is realized through the R packet of ChIPpeakAnno. The annotated results are available for download in csv format, as shown below.

Not only the corresponding gene annotation is given, but also downstream and other categories are defined according to the distance between peak and gene, in which the distance of promoter and enhancer can be customized.

For the distribution of different types of peak, a bar chart is also provided, as shown below

2. Peak to nearest peak distances

Draw the frequency distribution curve of the distance between peak and the corresponding gene, as shown below

At the same time, it can also be analyzed by multiple peak, including the following two results

1. Overlapping peak identifications

The intersection analysis of peak interval provides the quantitative statistics of intersection peak. The results are as follows.

2. Overlapping peak-associated genes

Venn analysis and functional enrichment analysis of peak associated genes are shown as follows

Online tools are easy to operate, especially for people who are not familiar with the R language. This online tool not only provides the same annotation results as CHIPpeakAnno, but also has more features, which is a good choice.

After reading the above, do you have any further understanding of annoPeakR, an online tool for peak annotations? If you want to know more knowledge or related content, please follow the industry information channel, thank you for your support.

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