Genrich | Detecting sites of genomic enrichment | Genomics library

by jsh58 C Version: v0.6.1 License: MIT

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

kandi X-RAY | Genrich Summary

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

Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.

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Security

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Support

Genrich has a low active ecosystem.

It has 150 star(s) with 27 fork(s). There are 10 watchers for this library.

It had no major release in the last 12 months.

There are 6 open issues and 89 have been closed. On average issues are closed in 107 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of Genrich is v0.6.1

Quality

Genrich has 0 bugs and 0 code smells.

Security

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

Genrich code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

Genrich is licensed under the MIT License. This license is Permissive.

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

Reuse

Genrich releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

It has 86 lines of code, 5 functions and 1 files.

It has low code complexity. Code complexity directly impacts maintainability of the code.

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Genrich Key Features

No Key Features are available at this moment for Genrich.

Genrich Examples and Code Snippets

No Code Snippets are available at this moment for Genrich.

Community Discussions

Trending Discussions on Genrich

Snakemake: {input:q} does not return quoted input

QUESTION

Snakemake: {input:q} does not return quoted input

Asked 2020-Oct-28 at 14:48

I am developing an ATACseq pipeline using Genrich to run with Snakemake.

The fact is that Genrich allows to call peaks from more than one replicate in the same step, avoiding additional steps (i.e. IDR).

In Snakemake, I have found the way to return all the samples I want (i.e. replicates from one condition) at the same time, but Genrich asks for comma-separated files as input or space-separated files if each file is quoted.

Normally, the input return a list of space-separated files (i.e. file1 file2 file3), and since I don't know how I can make it return comma-separated files, I tried to quote them.

In theory, after Snakemake version 5.8.0, you can refer to the input as {input:q} in the rule's shell command to return the quoted input, as said here.

However, in my case, the returned input is not quoted.

I have created a test rule to see how the input is returned:

...

ANSWER

Answered 2020-Oct-27 at 09:00

Assuming your input filenames do not contain spaces (and if they do I strongly encourage avoiding them), you can simply put the list of files in quotes, you don't need to quote each file in the list:

Source https://stackoverflow.com/questions/64546273

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

Vulnerabilities

No vulnerabilities reported

Install Genrich

To produce a file listing regions of genomic enrichment:.
sample.bam (alignment file, sorted by queryname)
Genrich (compiled as described below)

Support

Copyright © 2018 John M. Gaspar (jsh58@wildcats.unh.edu). Any question, concern, or bug report about the program should be posted as an Issue on GitHub. Before posting, please check previous issues (both Open and Closed) to see if your issue has been addressed already. Also, please follow these good GitHub practices.

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