Psichomics Versions Save

• Update GTEx data download based on new URL endpoints
• Documentation:
  • Update function documentation based on bug fixes below
  • Update license copyright years
• Bug fixes:
  • Fix deprecated used of size in ggplot2::geom_line
  • Fix inconsistent argument in survfit.survTerms()
  • Fix unit test issues when testing low coverage using random PSI values
  • Update pkgdown and R CMD check automation in GitHub Actions

• Bug fix: psichomics app now opens as expected instead of crashing

• Bug fix: GTEx data v8 can now be downloaded using newer versions of R
• Bug fix: UniProt REST API call now uses the updated API
• Bug fix: Updated deprecated setting to remove ggplot2 guide
• Documentation: Clarify how to get survival plots in CLI tutorial

Bug fix: fix limma-trend approach when using newer versions of limma to calculate average gene expression

Bug fix: correctly perform correlation analysis in the GUI after doing it once

• Alternative splicing event annotations:
  • Support new annotations from VAST-TOOLS for multiple species, including mouse, zebrafish, fruit fly, chicken, frog, C. elegans and A. thaliana
  • Automatically create cache directory if downloading splicing annotations for the first time
• Gene, transcript and protein annotation (visual interface):
  • Automatically set species/genome based on selected annotation
  • Improve species and genome selection

ShinyProxy support

• psichomics(): add argument shinyproxy; when set to TRUE, change set of options to viably run in ShinyProxy
• Avoid automatically closing the app
• Replace custom file browsers with shiny's versions
• Fix issues with progress bar
• Include ShinyBS JavaScript library
• Upload files using default file browser input and allow to upload a ZIP folder instead of a folder

Bug fixes

• Fix issues with Shiny 1.7.0:
  • Change icon names as required by newest versions of font-awesome
  • Avoid modifying Shiny tags using generic positions
• Load recount data (visual interface):
  • Improve responsiveness of project selection
• Splicing annotation (visual interface):
  • Load annotation only when opening the splicing quantification tab
  • Automatically select hg38 if using GTEx v8 data
• PCA plot (visual interface):
  • Automatically plot PCA after calculating PCA scores
  • Copy-edit text
  • Fix specific errors related with PCA analysis of only one group
• Diagrams of alternative splicing events:
  • Fix wrong coloring of reference exon used for AFE and A5SS events
• Transcript plot:
  • Orange region (the reference exon) is now on top of blue region

• Diagram of alternative splicing events:
  • Fix wrong colouring of reference exon used for AFE and A5SS events
• Transcript plot:
  • Avoid alternative regions from overlapping
  • Fix loading twice when selecting a new event (visual interface)

• psichomics(): fix visual interface not launching
  • getGtexReleases() not properly retrieving whether future GTEx releases (9 and higher) are available
• Remove warning related with TCGA data when MD5 checks fail

• plotSplicingEvent(): avoid opening browser window in non-interactive contexts
• Fix Bioconductor build report's timeout when creating vignettes on Windows