leafcutter | free quantification of RNA | Genomics library

by davidaknowles R Version: v0.2.7 License: Apache-2.0

X-Ray Key Features Code Snippets Community Discussions(2)Vulnerabilities Install Support

kandi X-RAY | leafcutter Summary

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

Yang I. Li1, David A. Knowles1, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard. Leafcutter quantifies RNA splicing variation using short-read RNA-seq data. The core idea is to leverage spliced reads (reads that span an intron) to quantify (differential) intron usage across samples. The advantages of this approach include. For details please see our bioRxiv preprint and corresponding Nature Genetics publication. Additionally, for full details on the leafcutter for Mendelian Diseases (leafcutterMD) method that performs outlier splicing detection, see our Bioinformatics publication. Full documentation is available at If you have usage questions we've setup a Google group here: We've developed a leafcutter shiny app for visualizing leafcutter results: you can view an example here. This shows leafcutter differential splicing results for a comparison of 10 brain vs. 10 heart samples (5 male, 5 female in each group) from GTEx.

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Support

leafcutter has a low active ecosystem.

It has 174 star(s) with 98 fork(s). There are 18 watchers for this library.

It had no major release in the last 12 months.

There are 70 open issues and 132 have been closed. On average issues are closed in 103 days. There are 6 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of leafcutter is v0.2.7

Quality

leafcutter has no bugs reported.

Security

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

License

leafcutter is licensed under the Apache-2.0 License. This license is Permissive.

Permissive licenses have the least restrictions, and you can use them in most projects.

Reuse

leafcutter releases are available to install and integrate.

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leafcutter Key Features

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leafcutter Examples and Code Snippets

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Community Discussions

Trending Discussions on leafcutter

Snakemake producing wildly incoherent error when dryrunning

How do I split a table into several new tables based on whether the column header matches with information found in another table? (R)

QUESTION

Snakemake producing wildly incoherent error when dryrunning

Asked 2019-Aug-19 at 08:10

I've spent the past year working on a project executed on a SLURM-managed cluster. Now we want to make our results reproducible and to do so, we're porting it to snakemake. However, I am learning it from scratch and it's giving me a headache.

Below is my code:

...

ANSWER

Answered 2019-Aug-16 at 20:58

Okay I decided to take the liberty to also give some style feedback while at it :). This is what I would make it (I ofcourse couldn't test it):

Source https://stackoverflow.com/questions/57528586

QUESTION

How do I split a table into several new tables based on whether the column header matches with information found in another table? (R)

Asked 2019-Jan-15 at 17:59

I have a table named NE that contains spliced RNA junctions:

...

ANSWER

Answered 2019-Jan-15 at 17:59

If you split Sample_Name by body_site, you get a vector of Sample_Names corresponding to each body_site. Then you just need to intersect this with the names of NE for each body_site, and select the columns resulting from that intersection. The result is a named list of data tables. The names are the body_site values.

Source https://stackoverflow.com/questions/54189236

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

Vulnerabilities

No vulnerabilities reported

Install leafcutter

You can download it from GitHub.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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