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)
SmartPhos 0.99.26 (2025-07-25)
SmartPhos 0.99.25 (2025-07-24)
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)
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)
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)
SmartPhos 0.99.9 (2025-03-18)
- update plotHeatmap() to reduce code repetition
SmartPhos 0.99.8 (2025-03-18)
SmartPhos 0.99.7 (2025-03-15)
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)
SmartPhos 0.99.3 (2025-02-26)
SmartPhos 0.99.2 (2025-02-26)
SmartPhos 0.99.1 (2025-02-26)
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