New version 1.6.0
 
+ Major package updates. It addresses most of the warnings and messages from required packages
+ Analysis of Protein Acetylation now supported.
+ General to all Quality control plots: update default names for all pdf outputs
+ QC artmsQualityControlEvidenceExtended():
   - New plots: peptide and protein overlap across bioreplicates and conditions (plotPEPTOVERLAP and plotPROTOVERLAP)
   - Updates and improves all the plots, affecting font size and other aesthetic options
   - Change parameter "plotIC" to "plotPCA" in artmsQualityControlEvidenceExtended()
+ QC artmsQualityControlEvidenceBasic():
   - Depracated: Plot correlation distributions
   - Updated and improved all the plots, affecting font size and other aesthetic
  + More data testing datasets available:
   - artms_data_ph_contrast: contrast object for available the PH example dataset
   - artms_data_ph_config: configuration yaml object for the available PH example dataset
   - artms_data_ph_msstats_results: results data object from running artmsQuantification
   - artms_data_ph_msstats_modelqc: modelqc data object from running artmsQuantification
+ Vignette updated
+ Other minor fixes / improvements

   
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
¡
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

