MetaboAnalystR | R package for MetaboAnalyst

by xia-lab R Version: v3.3.0 License: Non-SPDX

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

kandi X-RAY | MetaboAnalystR Summary

MetaboAnalystR is a R library. MetaboAnalystR has no bugs, it has no vulnerabilities and it has low support. However MetaboAnalystR has a Non-SPDX License. You can download it from GitHub.

MetaboAnalystR 3.0 contains the R functions and libraries underlying the popular MetaboAnalyst web server, including metabolomic data analysis, visualization, and functional interpretation. The package is synchronized with the MetaboAnalyst web server. After installing and loading the package, users will be able to reproduce the same results from their local computers using the corresponding R command history downloaded from MetaboAnalyst web site, thereby achieving maximum flexibility and reproducibility. The version 3.0 aims to improve the current global metabolomics workflow by implementing a fast parameter optimization algorithm for peak picking, and automated identification of the most suitable method for batch effect correction from 12 well-established approaches. In addition, more support for functional interpretation directly from m/z peaks via mummichog2 (PMID: 23861661), and a new pathway-based method to integrate multi'omics data has been added. To demonstrate this new functionality, we provide the "MetaboAnalystR 3.0 Workflow: Towards an Optimized Workflow for Global Metabolomics" vignette, available here as a PDF. In this vignette, we perform end-to-end metabolomics data analysis on the full batch of clinical IBD samples.

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Quality

Security

License

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Support

MetaboAnalystR has a low active ecosystem.

It has 240 star(s) with 137 fork(s). There are 21 watchers for this library.

It had no major release in the last 12 months.

There are 21 open issues and 233 have been closed. On average issues are closed in 410 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of MetaboAnalystR is v3.3.0

Quality

MetaboAnalystR has 0 bugs and 0 code smells.

Security

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

MetaboAnalystR code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

MetaboAnalystR 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

MetaboAnalystR releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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MetaboAnalystR Key Features

No Key Features are available at this moment for MetaboAnalystR.

MetaboAnalystR Examples and Code Snippets

No Code Snippets are available at this moment for MetaboAnalystR.

Community Discussions

Trending Discussions on MetaboAnalystR

How do I overcome issues with MetaboAnalyst in R when trying to run pathway analysis?

QUESTION

How do I overcome issues with MetaboAnalyst in R when trying to run pathway analysis?

Asked 2020-Jun-01 at 23:03

I am using this code https://drive.google.com/file/d/1CXluzyYqNoPqu1DI3HwvDAmRVGMe825m/view in order to undertake a pathway analysis using MetaboAnalystR.

When I get to this stage

...

ANSWER

Answered 2020-Jun-01 at 23:03

After spending at least 30 minutes installing dependencies from CRAN and Bioconductor, I was able to get the code to work.

If I had to guess your issue, you probably haven't installed all the dependency packages.

Follow the instructions here:

Source https://stackoverflow.com/questions/62119835

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

Vulnerabilities

No vulnerabilities reported

Install MetaboAnalystR

To use MetaboAnalystR 3.0, first install all package dependencies. Ensure that you have necessary system environment configured. For Linux (e.g. Ubuntu 18.04/20.04): libcairo2-dev, libnetcdf-dev, libxml2, libxt-dev and libssl-dev should be installed at frist;. For Windows (e.g. 7/8/8.1/10): Rtools should be installed. For Mac OS: In order to compile R for Mac OS, you need Xcode and GNU Fortran compiler installed. We suggest you follow these steps to help with your installation.
MetaboAnalystR 3.0 is freely available from GitHub. The package documentation, including the vignettes for each module and user manual is available within the downloaded R package file. You can install the MetaboAnalylstR 3.0 via any of the three options: A) using the R package devtools, B) cloning the github, C) manually downloading the .tar.gz file. Note that the MetaboAnalystR 3.0 github will have the most up-to-date version of the package. Due to issues with Latex, some users may find that they are only able to install MetaboAnalystR 3.0 without any documentation (i.e. vignettes). The * must be replaced by what is actually downloaded and built.

Support

To inform us of any bugs or requests, please open a new issue (and @ Zhiqiang-PANG !!) or send an email to #jasmine.chong@mail.mcgill.ca or zhiqiang.pang@mail.mcgill.ca.

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