NEWS

---

SmartPhos 0.99.30 (2025-10-01)

• update Namespace to include imputeLCMD

SmartPhos 0.99.29 (2025-10-01)

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

SmartPhos 0.99.28 (2025-07-31)

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

SmartPhos 0.99.27 (2025-07-25)

• no change

SmartPhos 0.99.26 (2025-07-25)

• add NEWS.txt file

SmartPhos 0.99.25 (2025-07-24)

• minor typo fix

SmartPhos 0.99.24 (2025-07-24)

• bug fix in enrichDifferential()

SmartPhos 0.99.23 (2025-07-24)

• update SmartPhos vignette

SmartPhos 0.99.22 (2025-07-22)

• add @return in dataset.R script return value

SmartPhos 0.99.21 (2025-07-22)

• minor typo fixes

SmartPhos 0.99.20 (2025-07-22)

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

SmartPhos 0.99.19 (2025-04-05)

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

SmartPhos 0.99.18 (2025-04-04)

• create data environment for correct data loading

SmartPhos 0.99.17 (2025-04-04)

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

SmartPhos 0.99.16 (2025-04-03)

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

SmartPhos 0.99.15 (2025-04-02)

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

SmartPhos 0.99.14 (2025-03-27)

• minor typo fixes

SmartPhos 0.99.13 (2025-03-21)

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

SmartPhos 0.99.12 (2025-03-21)

• update SmartPhos vignette

SmartPhos 0.99.11 (2025-03-20)

• update shiny server script
• simple code format

SmartPhos 0.99.10 (2025-03-20)

• simple code format

SmartPhos 0.99.9 (2025-03-18)

• update plotHeatmap() to reduce code repetition

SmartPhos 0.99.8 (2025-03-18)

• use @import instead of @importFrom for Namespace

SmartPhos 0.99.7 (2025-03-15)

• update DESCRIPTION file

SmartPhos 0.99.6 (2025-03-14)

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

SmartPhos 0.99.5 (2025-03-13)

• 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

SmartPhos 0.99.4 (2025-03-12)

• no change

SmartPhos 0.99.3 (2025-02-26)

• update gitignore file

SmartPhos 0.99.2 (2025-02-26)

• update gitignore file

SmartPhos 0.99.1 (2025-02-26)

• no change

SmartPhos 0.99.0 (2025-02-24)

• 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