Releases: nuno-agostinho/psichomics
Releases · nuno-agostinho/psichomics
1.28.1
- 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
inggplot2::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
- Fix deprecated used of
1.24.0
- Bug fix: psichomics app now opens as expected instead of crashing
1.22.1
- 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
1.20.2
Bug fix: fix limma-trend approach when using newer versions of limma to calculate average gene expression
1.20.1
Bug fix: correctly perform correlation analysis in the GUI after doing it once
1.20.0
- 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
1.18.6
ShinyProxy support
psichomics()
: add argumentshinyproxy
; when set toTRUE
, 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
1.18.5
- 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)
1.18.4
psichomics()
: fix visual interface not launchinggetGtexReleases()
not properly retrieving whether future GTEx releases (9 and higher) are available
- Remove warning related with TCGA data when MD5 checks fail
1.18.3
plotSplicingEvent()
: avoid opening browser window in non-interactive contexts- Fix Bioconductor build report's timeout when creating vignettes on Windows