Version 1.18 • psichomics

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)

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

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(): 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

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(): 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

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