ChIPseeker | : dart : ChIP peak Annotation , Comparison | Data Visualization library

by YuLab-SMU R Version: Current License: No License

X-Ray Key Features Code Snippets Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | ChIPseeker Summary

ChIPseeker is a R library typically used in Analytics, Data Visualization applications. ChIPseeker has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare their own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes. For details, please visit our project website,

Support

Quality

Security

License

Reuse

Support

ChIPseeker has a low active ecosystem.

It has 105 star(s) with 56 fork(s). There are 19 watchers for this library.

It had no major release in the last 6 months.

There are 63 open issues and 69 have been closed. On average issues are closed in 109 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of ChIPseeker is current.

Quality

ChIPseeker has no bugs reported.

Security

ChIPseeker has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

License

ChIPseeker does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

ChIPseeker releases are not available. You will need to build from source code and install.

Installation instructions are available. Examples and code snippets are not available.

Top functions reviewed by kandi - BETA

kandi's functional review helps you automatically verify the functionalities of the libraries and avoid rework.
Currently covering the most popular Java, JavaScript and Python libraries. See a Sample of ChIPseeker

Get all kandi verified functions for this library.

ChIPseeker Key Features

No Key Features are available at this moment for ChIPseeker.

ChIPseeker Examples and Code Snippets

No Code Snippets are available at this moment for ChIPseeker.

Community Discussions

Trending Discussions on ChIPseeker

Loop over a list of data frames to generate heatmaps and save them

QUESTION

Loop over a list of data frames to generate heatmaps and save them

Asked 2020-May-11 at 13:30

I have a list of data.frames called tagMatrixList from the package ChIPseeker. Is there a way to generate tagHeatmap (tagMatrixList, xlim=c(-3000, 3000), color="blue") for each data frame and then save each single plot in a file? Thank you in advance.

...

ANSWER

Answered 2020-May-11 at 13:30

You need to open up a image device to save the plot to it (such as png(), pdf(), etc.), and then close it with dev.off() when you're done.

Since your list doesn't have names and you want a file for each plot, we'll loop over a vector of numbers instead to both index the object, and add a file name with that index number.

Source https://stackoverflow.com/questions/61729046

Community Discussions, Code Snippets contain sources that include Stack Exchange Network