Roary | Rapid large-scale prokaryote pan genome analysis | Genomics library

by sanger-pathogens Perl Version: v3.13.0 License: Non-SPDX

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

kandi X-RAY | Roary Summary

Roary is a Perl library typically used in Artificial Intelligence, Genomics applications. Roary has no bugs, it has no vulnerabilities and it has low support. However Roary has a Non-SPDX License. You can download it from GitHub.

Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM.

Support

Quality

Security

License

Reuse

Support

Roary has a low active ecosystem.

It has 255 star(s) with 183 fork(s). There are 30 watchers for this library.

It had no major release in the last 12 months.

There are 151 open issues and 215 have been closed. On average issues are closed in 191 days. There are no pull requests.

It has a neutral sentiment in the developer community.

The latest version of Roary is v3.13.0

Quality

Roary has 0 bugs and 0 code smells.

Security

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

Roary code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

Roary has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

Roary releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

It has 645 lines of code, 2 functions and 2 files.

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

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Roary Key Features

No Key Features are available at this moment for Roary.

Roary Examples and Code Snippets

No Code Snippets are available at this moment for Roary.

Community Discussions

Trending Discussions on Roary

I want to use dplyr to filter a data frame if all members of a given group are absent

QUESTION

I want to use dplyr to filter a data frame if all members of a given group are absent

Asked 2021-Jun-08 at 20:57

I have a tab delimited binary matrix of bacterial strain names and genes, listed as present (1) or absent (0), which is output by ROARY (pangenome pipeline).

This is a mock version of the data:

...

ANSWER

Answered 2021-Jun-08 at 19:55

We can do a group by operation i.e. grouped by 'gene', check if all the 'a', 'b' are found in the 'strain' where the 'pres_abs' value is 0 and to avoid getting the 1 values in pres_abs, create a second condition i.e. 'pres_abs' as 0

Source https://stackoverflow.com/questions/67893730

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

Vulnerabilities

No vulnerabilities reported

Install Roary

Roary has the following dependencies:.

Support

We currently do not have the resources to provide support for Roary. However, the community might be able to help you out if you report any issues about usage of the software to the issues page.

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