Mercurial > repos > ethevenot > profia
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| author | ethevenot |
|---|---|
| date | Wed, 03 May 2017 10:49:08 -0400 |
| parents | 39ccace77270 |
| children | 3f8ae071bdda |
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Preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry data (FIA-HRMS) =============================================================================================================== A Galaxy module from the [Workflow4metabolomics](http://workflow4metabolomics.org) infrastructure Status: [](https://travis-ci.org/workflow4metabolomics/profia). ### Description **Version:** 3.0.4 **Date:** 2017-05-02 **Author:** Alexis Delabriere and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) **Citation:** Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. and Thevenot E.A. proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *submitted*. **Licence:** CeCILL **Reference history:** **Funding:** Agence Nationale de la Recherche ([MetaboHUB](http://www.metabohub.fr/index.php?lang=en&Itemid=473) national infrastructure for metabolomics and fluxomics, ANR-11-INBS-0010 grant) ### Installation * Configuration file: `profia_config.xml` * Image files: + `static/images/profia_workflowPositionImage.png` + `static/images/profia_workingExampleImage.png` * Wrapper file: `profia_wrapper.R` * R packages + **batch** from CRAN ```r install.packages("batch", dep=TRUE) install.packages("FNN", dep=TRUE) install.packages("maxLik", dep=TRUE) install.packages("minpack.lm", dep=TRUE) install.packages("pracma", dep=TRUE) ``` + **profia** from Bioconductor ```r source("http://www.bioconductor.org/biocLite.R") biocLite("xcms") biocLite("plasFIA") biocLite("proFIA") ``` ### Tests The code in the wrapper can be tested by running the `runit/profia_runtests.R` R file You will need to install **RUnit** package in order to make it run: ```r install.packages('RUnit', dependencies = TRUE) ``` ### Working example ### News ###### CHANGES IN VERSION 3.0.4 MINOR MODIFICATION * Details added in the documentation ###### CHANGES IN VERSION 3.0.2 NEW FEATURE * Parallel processing ###### CHANGES IN VERSION 3.0.0 NEW FEATURE * Creation of the tool