CHANGES IN VERSION 0.99.30 (2025-10-01)

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- update Namespace to include imputeLCMD


CHANGES IN VERSION 0.99.29 (2025-10-01)

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- perform imputation using MSCoreUtils package instead of DEP package
- update tests for basic_visualizations.R


CHANGES IN VERSION 0.99.28 (2025-07-31)

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- add download button in the shiny app to download the whole table  after performing differential expression
- minor code format


CHANGES IN VERSION 0.99.27 (2025-07-25)

- no change


CHANGES IN VERSION 0.99.26 (2025-07-25)

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- add NEWS.txt file


CHANGES IN VERSION 0.99.25 (2025-07-24)

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- minor typo fix


CHANGES IN VERSION 0.99.24 (2025-07-24)

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- bug fix in enrichDifferential()


CHANGES IN VERSION 0.99.23 (2025-07-24)

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- update SmartPhos vignette


CHANGES IN VERSION 0.99.22 (2025-07-22)

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- add @return in dataset.R script return value


CHANGES IN VERSION 0.99.21 (2025-07-22)

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- minor typo fixes


CHANGES IN VERSION 0.99.20 (2025-07-22)

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- add seesionInfo() in SmartPhos_Shiny vignette
- update DESCRIPTION file


CHANGES IN VERSION 0.99.19 (2025-04-05)

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- use seq_along() instead of 1:length() in runFisher()


CHANGES IN VERSION 0.99.18 (2025-04-04)

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- create data environment for correct data loading


CHANGES IN VERSION 0.99.17 (2025-04-04)

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- resolve verbose NOTE from devtools::check()
- minor typo fix in function argument


CHANGES IN VERSION 0.99.16 (2025-04-03)

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- add Depends in DESCRIPTION file
- add match.arg() in all relevant functions
- remove invalid unit tests


CHANGES IN VERSION 0.99.15 (2025-04-02)

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- update stop() message to fit 80-characters rule


CHANGES IN VERSION 0.99.14 (2025-03-27)

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- minor typo fixes


CHANGES IN VERSION 0.99.13 (2025-03-21)

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- remove @export from some functions
- add match.arg() in enrichDifferential()
- add unit tests for enrichDifferential()


CHANGES IN VERSION 0.99.12 (2025-03-21)

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- update SmartPhos vignette


CHANGES IN VERSION 0.99.11 (2025-03-20)

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- update shiny server script
- simple code format


CHANGES IN VERSION 0.99.10 (2025-03-20)

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- simple code format


CHANGES IN VERSION 0.99.9 (2025-03-18)

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- update plotHeatmap() to reduce code repetition 


CHANGES IN VERSION 0.99.8 (2025-03-18)

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- use @import instead of @importFrom for Namespace


CHANGES IN VERSION 0.99.7 (2025-03-15)

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- update DESCRIPTION file


CHANGES IN VERSION 0.99.6 (2025-03-14)

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- code format
- update warning() to stop() and update unit tests accordingly
- create data environment to use in-package dataset


CHANGES IN VERSION 0.99.5 (2025-03-13)

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- update color argument to colorByCol in plotIntensity()
- add verbose argument in readExperiment() and readExperimentDIA()
- update names of in-package datasets
- remove print() inside functions and add message() with verbose argument


CHANGES IN VERSION 0.99.4 (2025-03-12)

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- no change


CHANGES IN VERSION 0.99.3 (2025-02-26)

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- update gitignore file


CHANGES IN VERSION 0.99.2 (2025-02-26)

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- update gitignore file


CHANGES IN VERSION 0.99.1 (2025-02-26)

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- no change


VERSION 0.99.0 (2025-02-24)

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- SmartPhos package with shinyApp SmartPhos Explorer
- create MultiAssayExperiment object from Spectronaut & MaxQuant files
- different visualization and analysis available.
- possible analysis:
  - data transformation and normalization
  - data imputation
  - batch effect correction
  - principal component analyis
  - differential expression analyis
  - time-series clustering
  - geneset enrichment analyis
  - phopho-signature enrichment 
  - kinase activity inference
- visualizations:
  - intensity plot
  - pca plot
  - heatmaps
  - volacano plot for differential expression analysis
  - p value histogram
  - time series plot
  - geneset enrichment plots
  - kinase activity inference