Changes in version 1.10.2 (2021-07-13)
+ Bug fix affecting {artmsAnalysisQuantifications()}
+ Allow {artmsAnalysisQuantifications()} to process previous versions of artMS
+ Change Extension of {artms_sessionInfo_quantification} file from {.txt} to {.log}
+ New parameters available in {artmsQuantification()}, including:
   - Parameter {printTables}. Default {TRUE}, prints tables. FALSE otherwise.
   - Parameter {return_results_object}. If TRUE, it returns a list of data frames with MSstats results. Default is FALSE
   - If both {printTables} and {printPDF} are FALSE, then {return_results_object} becames TRUE and a list of data frames is returned
+ Change default parameters of the configuration files: less verbose

Changes in version 1.10.1 (2021-06-30)
+ Addressing major changes in MSstats
   - R version larger than 4.1 is now required
   - Fractions: the option "Fractions" is removed from the configuration file. If fractions are present, the user must include a "Fraction" column in the keys.txt file, which artMS will detect automatically.
   - {artmsQualityControlEvidenceBasic}: fraction parameter no longer required (automatically detected from the keys file)
   - {keys.txt}: use {Fraction} instead of {FractionKey}
+ External packages used exclusively by the {artmsAnalysisQuantifications} function are not required. Those packages will have to be installed before running this function.
+ {artmsAvgIntensityRT}: argument {species} is not longer required
+ Example datasets: 
   - {artms_data_ph_evidence}: the size has been significantly reduced (bioconductor requirement). Only two biological replicates and 1/20 of the lines selected randomly. Including only 36 columns from the original evidence file
   - {artms_data_ph_msstats_results}: output from running {artmsQuantification} on the full version of the evidence file, including 4 biological replicates (instead of the reduced version available in the package)
   - {artms_data_ph_msstats_modelqc}: output from running {artmsQuantification} on the full version of the evidence file, including 4 biological replicates (instead of the reduced version available in the package)

Changes in version 1.10.0 (2021-05-12)
+ Bioconductor release 3.13
+ Several adjustments in {artmsAnalysisQuantifications} function:
   - Use NAs instead of 0 when reshaping the data for missing values ({-log2fc-wide.txt} and {-log2fc-long.txt} files)
   - {plotClusteringAnalysis} only available when 3 or more comparisons available in the configuration file
+ R > v4.0.0 is now required
+ Update documentation & vignette
+ Code cleaning

Changes in version 1.8.3 (2021-04-05)
+ {artmsProtein2SiteConversion} now supports uniprot id isoforms (thanks Emily King)
+ Update vignette to make clearer how to provide several protein ids in "normalization_reference" (thanks Olga Schubert)

Changes in version 1.8.2 (2021-03-18)
+ {artmsProtein2SiteConversion}: New PTM available as argument, a new user defined `PTM:XXX:yy`. Check documentation to find out more
+ QC plots: by default, all qc plots are now output to a folder directory, by type (qc-basic, qc-extended, qc_summary)
+ artMS working directory: artMS will create all the folders and subfolders relative to the working directory. No need to specify the full path to the working directory, but the user must set the working directory: setwd("/path/to/working/directory/")
+ Configuration file data object updates:
   + "output" the user can add a folder where would like to have the output results file. For example, "output: results_202003/example-results.txt" would create the "resutls_202003" folder (if it does not exist) with all the results files available there
   + "LFC" (log2fc) updated to range -0.58 to 0.58, i.e., a fold change larger than a 1.5 (instead of 2 as before)
+ Update and improve documentation and vignette
+ Several bug fixes

Changes in version 1.8.1 (2020-10-27)
+ Update "plotPCA" message
+ Update documentation and vignettes
+ Code cleaning

Changes in version 1.8.0 (2020-10-27)
+ New bioconductor version

Changes in version 1.6.7 (2020-10-22)
+ The following plots are now deprecated
   + .clustering.log2fcSign.all-zoom.pdf
   + .clustering.log2fc.all-zoom.pdf 
+ Fix bugs

Changes in version 1.6.6 (2020-10-21)
+ Convert new MaxQuant format of PTMs to the old format
+ MSstats messages are not displayed by default when using artmsQuantification. 
The user can enable MSstats messages by selecting "display_msstats = TRUE"
+ Prevent artmsWriteConfigYamlFile() from overwriting an existing configuration
file unless the user allows it (overwrite = TRUE)
+ printPDF now available in all functions printing plots to pdf, which means that
notebooks can be used and print all plots. Default is still printPDF = TRUE
+ Fix bugs 

Changes in version 1.6.5 (2020-05-20)
+ Fix ggplot warnings (caused by NA values)
+ Fix artmsAnalysisQuantification reproducibility plots
+ Improves artmsQualityControlEvidenceBasic() correlation matrix clustered plot
+ Fix pca01.pdf plot
+ New pca04.pdf plot (dot plot)
+ artmsAnalysisQuantifications check point: check if sufficient data is available

Changes in version 1.6.4 (2020-05-12)
+ Fix Quality Control functions to handle a small number of runs (less than 5)
+ New argument "printPDF" for artmsQualityControlSummaryExtended, to select
whether to print plots to PDFs (default = TRUE)
+ Vignette: example plots added

Changes in version 1.6.3 (2020-05-06)
+ Bug Fixes affecting artmsAnalysisQuantifications()

Changes in version 1.6.2 (2020-05-05)
+ Fix NEWS formatting 
+ Update vignette with AC options

Changes in version 1.6.1 (2020-04-29)
+ Fix NEWS formatting 
+ Update vignette with AC options

Changes in version 1.6.0 (2020-04-27)
+ 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
   
Changes in 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()

Changes in version 1.4.2 (2019-12-06)
+ Fixed a crash when impute fails due to missing outlier data (part 2)

Changes in version 1.4.1 (2019-12-06)
+ Fixed a crash when impute fails due to missing outlier data

Changes in version 1.4.0 (2019-11-01)
+ New bioconductor release

Changes in version 1.2.9 (2019-10-28)
+ Bug fix on artmsProtein2SiteConversion affecting UB conversion

Changes in 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.

Changes in version 1.2.7 (2019-10-14)
+ Remove reshape2 dependency (depracated) and use 
data.table melt function instead
+ Update documentation: Notes on imputation

Changes in 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

Changes in version 1.2.5 (2019-07-25)
+ Update vignette and readme

Changes in version 1.2.4 (2019-07-25)
+ artMS requires now R > 3.6
+ Check point for empty evidence files

Changes in 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)

Changes in 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

Changes in version 1.2.1 (2019-05-07)
+ Fix artmsProtein2SiteConversion package dependency

Changes in version 1.2.0 (2019-05-01)
+ Bioconductor release: update version (from 1.1 to 1.3)

Changes in version 1.0.17 (2019-05-27)
+ Minor changes in code

Changes in version 1.0.16 (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 1.0.15 (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 1.0.14 (2019-04-22)
+ Update artmsProtein2SiteConversion: it runs as default the "Leading razor protein".
+ Update vignette

Changes in version 1.0.13 (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 1.0.12 (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 1.0.11 (2019-03-25)
+ Fix: column namne MS/MS count for old versions of MaxQuant

Changes in version 1.0.10 (2019-02-22)
+ Fix: final fix of build problems

Changes in version 1.0.9 (2019-02-21)
+ Fix: build problem

Changes in version 1.0.8 (2019-02-18)
+ Fix: Remove abundance files to prevent users' confusions
+ Fix: use "Leading Razor Protein" as main protein ID

Changes in version 1.0.7 (2019-02-18)
+ Bug fix: update annotations to process species without support by bioconductor
annotation packages.
+ Improve messages to the user

Changes in version 1.0.6 (2019-01-21)
+ Bug fix (checkfile)

Changes in version 1.0.5 (2019-01-20)
+ Update the vignette

Changes in version 1.0.3 (2019-01-20)
+ bug fix: pre-formatted mss file now works

Changes in version 1.0.2 (2019-01-19)
+ Fixed error: the condition has length (from bioc 3.9)
+ Fixed bug with artmsVolcanoPlot

Changes in version 1.0.1 (2018-10-29)
+ Fixed bug on artmsProtein2SiteConvertion

Changes in version 1.0.0 (2018-10-29)
+ artMS is officially released

Changes in version 0.99.102 (2018-10-27)
+ Fix bug in artmsConvertMetabolomics()

Changes in version 0.99.101
+ Update vignettes

Changes in version 0.99.100
+ 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 0.99.52
+ 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
