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psichomics 1.18.0 (18 May, 2021)

  • discardLowCoveragePSIvalues(): improve performance (2x faster)
  • When quantifying or loading PSI values, psichomics discards splicing events whose junctions:
      1. are not present in junction quantification data or
      1. have low numbers of reads across all samples. The number of discarded events is now displayed during PSI quantification.
  • When normalizing gene expression, support converting gene identifiers to gene symbol names for any species with OrgDb data
  • Allow to use plotSplicingEvent() directly with a PSI table to plot diagrams of the alternative splicing events within
  • Distribution plots (plotDistribution()):
    • Plot sample distributions in density, violin or box plots (argument type in command-line interface)
    • Hide rug plot when showing 500 or more values (by default) to avoid performance issues
    • Add jitter to rug plot (helps to discern numerous points)
    • Display interquartile range (IQR) per group in the tooltip
    • Add subtitles (argument subtitle in command-line interface)
    • Allow to invert axes (argument invertAxes in command-line interface)

Bug fixes and minor changes

  • loadLocalFiles(): print elapsed time after loading local files
  • filterGroups() was modified to return a character vector whose names are original names (instead of groups) and include an attribute Groups with the respective group of each value (together with their colour, if available):
    • Distribution plots in the graphical interface now show sample name in the tooltip for each sample
  • Importing VAST-TOOLS annotation:
    • Fix parsing of VAST-TOOLS intron retention events as skipped exon for certain annotations (including Hs2)
    • Support diagrams for intron retention events with full exon coordinates
  • Graphical user interface improvements:
    • Avoid “Matching subjects to their samples/Matching process concluded” loop
    • Timeout GTEx data retrieval after 3 seconds without server response
    • Avoid unnecessary messages when loading FireBrowse interface
    • Fix intron retention diagrams in distribution plots not displaying introns
    • When searching for specific splicing events, fix results based on the wrong genomic coordinates
  • Improve tutorials

psichomics 1.18.1 (26 May, 2021)

  • Fix issues with unit tests in Bioconductor
  • Improve Docker images:
    • Simplify Dockerfile
    • Store Docker images in GitHub Container Registry
    • Automatically build latest Docker image based on last release version
  • Improve README with install instructions for GitHub and Docker
  • Minor copy-editing of user-provided data tutorial
  • Fix minor spelling issues

psichomics 1.18.3 (11 June, 2021)

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

psichomics 1.18.4 (22 July, 2021)

  • 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

psichomics 1.18.5 (24 August, 2021)

  • Diagrams of alternative splicing events:
    • Fix wrong coloring 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 1.18.6 (4 October, 2021)

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