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planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
author ethevenot
date Mon, 22 Jan 2018 11:32:41 -0500
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6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/profia.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/profia). 6 Status: [![Build Status](https://travis-ci.org/workflow4metabolomics/profia.svg?branch=master)](https://travis-ci.org/workflow4metabolomics/profia).
7 7
8 ### Description 8 ### Description
9 9
10 **Version:** 3.0.4 10 **Version:** 3.1.0
11 **Date:** 2017-05-02 11 **Date:** 2018-01-08
12 **Author:** Alexis Delabriere and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team) 12 **Author:** Alexis Delabriere and Etienne A. Thevenot (CEA, LIST, MetaboHUB, W4M Core Development Team)
13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr) 13 **Email:** [etienne.thevenot(at)cea.fr](mailto:etienne.thevenot@cea.fr)
14 **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*. 14 **Citation:** Delabriere A., Hohenester U., Colsch B., Junot C., Fenaille F. and Thevenot E.A. (2017). proFIA: A data preprocessing workflow for Flow Injection Analysis coupled to High-Resolution Mass Spectrometry. *Bioinformatics*, 33:3767-3775 (https://doi.org/10.1093/bioinformatics/btx458).
15 **Licence:** CeCILL 15 **Licence:** CeCILL
16 **Reference history:** 16 **Reference history:**
17 **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) 17 **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)
18 18
19 ### Installation 19 ### Installation
26 * R packages 26 * R packages
27 + **batch** from CRAN 27 + **batch** from CRAN
28 28
29 ```r 29 ```r
30 install.packages("batch", dep=TRUE) 30 install.packages("batch", dep=TRUE)
31 install.packages("FNN", dep=TRUE)
32 install.packages("maxLik", dep=TRUE)
33 install.packages("minpack.lm", dep=TRUE) 31 install.packages("minpack.lm", dep=TRUE)
32 install.packages("missForest", dep=TRUE)
34 install.packages("pracma", dep=TRUE) 33 install.packages("pracma", dep=TRUE)
35 ``` 34 ```
36 + **profia** from Bioconductor 35 + **profia** from Bioconductor
37 36
38 ```r 37 ```r
39 source("http://www.bioconductor.org/biocLite.R") 38 source("http://www.bioconductor.org/biocLite.R")
39 biocLite("Biobase")
40 biocLite("BiocParallel")
40 biocLite("xcms") 41 biocLite("xcms")
41 biocLite("plasFIA") 42 biocLite("plasFIA")
42 biocLite("proFIA") 43 biocLite("proFIA")
43 ``` 44 ```
44 45
53 54
54 ### Working example 55 ### Working example
55 56
56 ### News 57 ### News
57 58
59 ###### CHANGES IN VERSION 3.1.0
60
61 NEW FEATURE
62
63 randomForest method implemented for imputation of missing values
64
65 ###### CHANGES IN VERSION 3.0.6
66
67 NEW FEATURES
68
69 * New (advanced) parameters available
70
58 ###### CHANGES IN VERSION 3.0.4 71 ###### CHANGES IN VERSION 3.0.4
59 72
60 MINOR MODIFICATION 73 MINOR MODIFICATION
61 74
62 * Details added in the documentation 75 * Details added in the documentation