methylKit | R package for DNA methylation analysis | Genomics library

by al2na R Version: v0.99.2 License: No License

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

kandi X-RAY | methylKit Summary

methylKit is a R library typically used in Artificial Intelligence, Genomics applications. methylKit has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

methylKit is an [R] package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from [RRBS] and its variants, but also target-capture methods such as [Agilent SureSelect methyl-seq] In addition, methylKit can deal with base-pair resolution data for 5hmC obtained from Tab-seq or oxBS-seq. It can also handle whole-genome bisulfite sequencing data if proper input format is provided.

Support

Quality

Security

License

Reuse

Support

methylKit has a low active ecosystem.

It has 157 star(s) with 92 fork(s). There are 15 watchers for this library.

It had no major release in the last 12 months.

There are 43 open issues and 163 have been closed. On average issues are closed in 247 days. There are 5 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of methylKit is v0.99.2

Quality

methylKit has no bugs reported.

Security

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

License

methylKit 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

methylKit releases are available to install and integrate.

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

Get all kandi verified functions for this library.

methylKit Key Features

No Key Features are available at this moment for methylKit.

methylKit Examples and Code Snippets

No Code Snippets are available at this moment for methylKit.

Community Discussions

Trending Discussions on methylKit

How can I get my labels to move with my data?

QUESTION

How can I get my labels to move with my data?

Asked 2018-Feb-14 at 19:14

I am currently using MethylKit to analyze and plot my data and I would like to use visualize my data. I am working on a server and have automated the script and it seems that while the plot will change, the location of the labels will not, as seen in the two plots I've attached below.

My code is as follows:

...

ANSWER

Answered 2018-Feb-14 at 19:14

Since you do not specify the y coordinate in you text call, what happens is that "if y is missing, xy.coords(x, y) is used for construction of the coordinates."

When xy.coords is passed a data.frame or matrix, it assumes that the 1st column is x, and the 2nd is y. In your example, this means that project.pca$x which contains coordinates for all of the principal components is interpreted in both calls to text as providing the x,y coordinates in its first two columns.

So, to get the correct coordincates for PC1 and PC3, you can use

Source https://stackoverflow.com/questions/48794090

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

Vulnerabilities

No vulnerabilities reported

Install methylKit

You can download it from GitHub.

Support

You can look at the vignette [here](https://bioconductor.org/packages/release/bioc/vignettes/methylKit/inst/doc/methylKit.html). This is the primary source of documentation. It includes detailed examples. You can check out the [slides](https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/methylkit/methylKitTutorialSlides_2013.pdf ) for a tutorial at EpiWorkshop 2013. This works with older versions of methylKit, you may need to update the function names. You can check out the [tutorial](https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/methylkit/methylKitTutorial_feb2012.pdf) prepared for EpiWorkshop 2012. This works with older versions of methylKit, you may need to update the function names. You can check out the [slides](https://www.slideshare.net/AlexanderGosdschan/eurobioc-2018-metyhlkit-overview) prepared for EuroBioc 2018. This also includes more recent features of methylKit and is meant to give you a quick overview about what you can do with the package.

Find more information at: