Mercurial > repos > ethevenot > profia
comparison README.md @ 2:3f8ae071bdda draft
planemo upload for repository https://github.com/workflow4metabolomics/profia.git commit 19ed25c048232776369a392ddb8c1860471acd29
author | ethevenot |
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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 |