CRISPResso | Software pipeline for the analysis of CRISPR-Cas9 genome | Genomics library

by lucapinello Python Version: 1.0.13 License: AGPL-3.0

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

kandi X-RAY | CRISPResso Summary

CRISPResso is a Python library typically used in Artificial Intelligence, Genomics, Docker applications. CRISPResso has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can install using 'pip install CRISPResso' or download it from GitHub, PyPI.

Software pipeline for the analysis of CRISPR-Cas9 genome editing outcomes from sequencing data

Support

Quality

Security

License

Reuse

Support

CRISPResso has a low active ecosystem.

It has 117 star(s) with 47 fork(s). There are 9 watchers for this library.

It had no major release in the last 12 months.

There are 1 open issues and 45 have been closed. On average issues are closed in 18 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of CRISPResso is 1.0.13

Quality

CRISPResso has 0 bugs and 0 code smells.

Security

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

CRISPResso code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

CRISPResso is licensed under the AGPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

CRISPResso releases are available to install and integrate.

Deployable package is available in PyPI.

Build file is available. You can build the component from source.

CRISPResso saves you 1601 person hours of effort in developing the same functionality from scratch.

It has 3558 lines of code, 103 functions and 15 files.

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

Top functions reviewed by kandi - BETA

kandi has reviewed CRISPResso and discovered the below as its top functions. This is intended to give you an instant insight into CRISPResso implemented functionality, and help decide if they suit your requirements.

Install the dependencies
Check if needle is installed
Check if flash is installed
Find the path to the named executable
Check if a tool has been installed

Get all kandi verified functions for this library.

CRISPResso Key Features

No Key Features are available at this moment for CRISPResso.

CRISPResso Examples and Code Snippets

No Code Snippets are available at this moment for CRISPResso.

Community Discussions

Trending Discussions on CRISPResso

Iterating Over Strings in Shell Commands Using Snakemake

QUESTION

Iterating Over Strings in Shell Commands Using Snakemake

Asked 2019-Dec-18 at 19:27

To give a little background, I'm trying to put together a pipeline to analyze deep sequencing results of in-silico predicted CRISPR off targets. I amplify a known sequence from the genome in 50 different places and each amplicon contains a predicted off target site where my original CRISPR guide could potentially bind. I input the two paired end NGS files into the program CRISPResso along with the amplicon sequence and off-target guide. The two paired end files, amplicon sequence, and gRNA are different for each of the 50 sites. I need to do this with multiple conditions, donors, and replicates so the numbers add up quick.

I created the snakemake workflow below:

...

ANSWER

Answered 2019-Dec-15 at 13:51

The config file you show should have a space after the hyphen, i.e.:

Source https://stackoverflow.com/questions/59342187

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

Vulnerabilities

No vulnerabilities reported

Install CRISPResso

You can install using 'pip install CRISPResso' or download it from GitHub, PyPI.
You can use CRISPResso like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

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 .

Find more information at: