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Repository xcms_retcor
Name: xcms_retcor
Owner: lecorguille
Synopsis: [Metabolomics][W4M][LC-MS] XCMS R Package - Preprocessing - Correct retention time from different samples
Part of the W4M project: http://workflow4metabolomics.org XCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html Retention Time Correction using retcor function from xcms R package
Type: unrestricted
Revision: 21:7faadba7c625
This revision can be installed: True
Times cloned / installed: 914

Repository README files - may contain important installation or license information

Changelog/News -------------- .. _News: https://bioconductor.org/packages/release/bioc/news/xcms/NEWS **Version 3.4.4.1 - 30/04/2019** - BUGFIX: remove the pre-compute of the chromatograms which was memory consuming. Now, only xcms plot chromatogram will generate the Chromatograms. **Version 3.4.4.0 - 08/02/2019** - UPGRADE: upgrade the xcms version from 3.0.0 to 3.4.4 (see XCMS News_) **Version 3.0.0.0 - 08/03/2018** - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods. Some parameters may have been renamed. - NEW: a bunch of new options: Obiwarp.(centerSample, response, distFun, gapInit, gapExtend, factorDiag, factorGap, localAlignment, initPenalty) - IMPROVEMENT: the advanced options are now in sections. It will allow you to access to all the parameters and to know their default values. - CHANGE: removing of the TIC and BPC plots. You can new use the dedicated tool "xcms plot chromatogram" **Version 2.1.1 - 29/11/2017** - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C **Version 2.1.0 - 03/02/2017** - IMPROVEMENT: xcms.retcor can deal with merged individual data **Version 2.0.8 - 22/12/2016** - BUGFIX: when having only one group (i.e. one folder of raw data) the BPC and TIC pdf files do not contain any graph **Version 2.0.7 - 06/07/2016** - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 **Version 2.0.6 - 04/04/2016** - TEST: refactoring to pass planemo test using conda dependencies **Version 2.0.5 - 10/02/2016** - BUGFIX: better management of errors. Datasets remained green although the process failed - BUGFIX: some pdf remained empty even when the process succeed - UPDATE: refactoring of internal management of inputs/outputs - UPDATE: refactoring to feed the new report tool **Version 2.0.2 - 02/06/2015** - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors. - IMPROVEMENT: parameter labels have changed to facilitate their reading.
Dependencies of this repository

Repository no_unzip_datatype revision 7800ba9a4c1e owned by lecorguille
Repository rdata_xcms_datatypes revision 544f6d2329ac owned by lecorguille

Contents of this repository

Name Description Version Minimum Galaxy Version
Retention Time Correction 3.4.4.1 16.01

Categories
Metabolomics - Tools for use in the study of Metabolomics