New version 1.4.3 (2020-02-08) + artmsAnalysisQuantifications(), several updates: - change default value for "l2fc_thres" to 1 - change defult value for "output_dir" to "analysis_quant" - NEW option: "outliers". It allows to remove outliers from abundance data + Fix bug affecting artmsQualityControlSummaryExtended() New version 1.4.2 (2019-12-06) + Fixed a crash when impute fails due to missing outlier data (part 2) New version 1.4.1 (2019-12-06) + Fixed a crash when impute fails due to missing outlier data New version 1.4.0 (2019-11-01) + New bioconductor release New version 1.2.9 (2019-10-28) + Bug fix on artmsProtein2SiteConversion affecting UB conversion New version 1.2.8 (2019-10-21) + Enhancement: artmsProtein2SiteConversion can handle now full uniprot ids (as extracted by default in MaxQuant). For example, from sp|Q86U42|PABP2_HUMAN it will extract the Uniprot entry id Q86U42 as the main id and the "protein to site"" conversion is performed. New version 1.2.7 (2019-10-14) + Remove reshape2 dependency (depracated) and use data.table melt function instead + Update documentation: Notes on imputation New version 1.2.6 (2019-08-01) + Optimize Analysis of Quantifications: adding check points when enrichment tool gProfileR is not available; clean up code; fix bugs New version 1.2.5 (2019-07-25) - Update vignette and readme New version 1.2.4 (2019-07-25) - artMS requires now R > 3.6 - Check point for empty evidence files New version 1.2.3 (2019-06-11) + Fix: Refactored code to better handle SILAC data in QC and quantifications + New function to hack SILAC data + Keeps adding `na.rm = TRUE` to ggplots + Improves QC plots + Overall code formating (going back to my prefered style) New version 1.2.2 (2019-05-11) + Fix: add PH check for new maxquant versions in basic QC plot function + New function to add error bars in plots New version 1.2.1 (2019-05-07) + Fix artmsProtein2SiteConversion package dependency New version 1.2.0 (2019-05-01) + Bioconductor release: update version (from 1.1 to 1.3) Changes in version v1.0.17 (2019-05-27) + Minor changes in code Changes in version v1.0.16 (2019-04-27) + The configuration file also includes the option to activate quality control based on the summary.txt file + Improve messages to the user Changes in version v1.0.15 (2019-04-24) + artMS detects RefSeq IDs. It does not support yet enrichments and annotations + Update artmsAnalysisQuantifications to adjust for previous changes in PTMs: it better handles 'protein groups' + Doesn't remove outliers Changes in version v1.0.14 (2019-04-22) + Update artmsProtein2SiteConversion: it runs as default the "Leading razor protein". + Update vignette Changes in version v1.0.13 (2019-04-20) + Important artmsProtein2SiteConversion update: the protein column id to be converted to the 'site/peptide specific' notation (i.e. ProteinID_AAnumber) can be now selected by the user. This is important because if the user decides to remove the protein groups, the 'leading razor protein' is chosen as the main protein id column, therefore the user would have to choose that protein when converting the file. + artmsQuantification is now able to process full uniprot ids (sp|ENTRY|ENTRY_NAME ...): it detects and extracts the ENTRY id + Depracated: artmsReplicatePlots Changes in version v1.0.12 (2019-04-07) + Fix: filtering by group uses the Leading Razor Protein when the filter "protein_groups: remove" is selected + Fix: `plotSP` of `artmsQualityControlEvidenceExtended` fails with old versions of MaxQuant + artmsProtein2SiteConversion also processes RefSeq annotations Changes in version v1.0.11 (2019-03-25) + Fix: column namne MS/MS count for old versions of MaxQuant Changes in version v1.0.10 (2019-02-22) + Fix: final fix of build problems ยก Changes in version v1.0.9 (2019-02-21) + Fix: build problem Changes in version v1.0.8 (2019-02-18) + Fix: Remove abundance files to prevent users' confusions + Fix: use "Leading Razor Protein" as main protein ID Changes in version v1.0.7 (2019-02-18) + Bug fix: update annotations to process species without support by bioconductor annotation packages. + Improve messages to the user Changes in version v1.0.6 (2019-01-21) + Bug fix (checkfile) Changes in version v1.0.5 (2019-01-20) + Update the vignette Changes in version v1.0.3 (2019-01-20) + bug fix: pre-formatted mss file now works Changes in version v1.0.2 (2019-01-19) + Fixed error: the condition has length (from bioc 3.9) + Fixed bug with artmsVolcanoPlot Changes in version v1.0.1 (2018-10-29) + Fixed bug on artmsProtein2SiteConvertion Changes in version v1.0.0 (2018-10-29) + artMS is officially released Changes in version v0.99.102 (2018-10-27) + Fix bug in artmsConvertMetabolomics() Changes in version v0.99.101 + Update vignettes Changes in version v0.99.100 + This version addresses all the suggestions and comments raised by the bioconductor's reviewer + Incorporates functions to handle Metabolomics based on the Markview alignment table Changes in version v0.99.52 + Updated Vignette extensively Changes in version 0.99.25 + Update Vignette to just output html Changes in version 0.99.02 + Add the Bioconductor webhook Changes in version 0.99.01 + Submit the package to the Bioconductor project For Developers + All the functions name must have the prefix 'artms' + Normalized all documentation using roxygen2 Deprecated + Nothing yet Defunct + Nothing yet