Changes in version 0.99.30 (2025-10-01) o update Namespace to include imputeLCMD Changes in version 0.99.29 (2025-10-01) o perform imputation using MSCoreUtils package instead of DEP package o update tests for basic_visualizations.R Changes in version 0.99.28 (2025-07-31) o add download button in the shiny app to download the whole table after performing differential expression o minor code format Changes in version 0.99.27 (2025-07-25) o no change Changes in version 0.99.26 (2025-07-25) o add NEWS.txt file Changes in version 0.99.25 (2025-07-24) o minor typo fix Changes in version 0.99.24 (2025-07-24) o bug fix in enrichDifferential() Changes in version 0.99.23 (2025-07-24) o update SmartPhos vignette Changes in version 0.99.22 (2025-07-22) o add @return in dataset.R script return value Changes in version 0.99.21 (2025-07-22) o minor typo fixes Changes in version 0.99.20 (2025-07-22) o add seesionInfo() in SmartPhos_Shiny vignette o update DESCRIPTION file Changes in version 0.99.19 (2025-04-05) o use seq_along() instead of 1:length() in runFisher() Changes in version 0.99.18 (2025-04-04) o create data environment for correct data loading Changes in version 0.99.17 (2025-04-04) o resolve verbose NOTE from devtools::check() o minor typo fix in function argument Changes in version 0.99.16 (2025-04-03) o add Depends in DESCRIPTION file o add match.arg() in all relevant functions o remove invalid unit tests Changes in version 0.99.15 (2025-04-02) o update stop() message to fit 80-characters rule Changes in version 0.99.14 (2025-03-27) o minor typo fixes Changes in version 0.99.13 (2025-03-21) o remove @export from some functions o add match.arg() in enrichDifferential() o add unit tests for enrichDifferential() Changes in version 0.99.12 (2025-03-21) o update SmartPhos vignette Changes in version 0.99.11 (2025-03-20) o update shiny server script o simple code format Changes in version 0.99.10 (2025-03-20) o simple code format Changes in version 0.99.9 (2025-03-18) o update plotHeatmap() to reduce code repetition Changes in version 0.99.8 (2025-03-18) o use @import instead of @importFrom for Namespace Changes in version 0.99.7 (2025-03-15) o update DESCRIPTION file Changes in version 0.99.6 (2025-03-14) o code format o update warning() to stop() and update unit tests accordingly o create data environment to use in-package dataset Changes in version 0.99.5 (2025-03-13) o update color argument to colorByCol in plotIntensity() o add verbose argument in readExperiment() and readExperimentDIA() o update names of in-package datasets o remove print() inside functions and add message() with verbose argument Changes in version 0.99.4 (2025-03-12) o no change Changes in version 0.99.3 (2025-02-26) o update gitignore file Changes in version 0.99.2 (2025-02-26) o update gitignore file Changes in version 0.99.1 (2025-02-26) o no change Changes in version 0.99.0 (2025-02-24) o SmartPhos package with shinyApp SmartPhos Explorer o create MultiAssayExperiment object from Spectronaut & MaxQuant files o different visualization and analysis available. o possible analysis: o data transformation and normalization o data imputation o batch effect correction o principal component analyis o differential expression analyis o time-series clustering o geneset enrichment analyis o phopho-signature enrichment o kinase activity inference o visualizations: o intensity plot o pca plot o heatmaps o volacano plot for differential expression analysis o p value histogram o time series plot o geneset enrichment plots o kinase activity inference