getSplicingEventData(): get a table with all information for a given dataset of alternative splicing quantification data
VAST-TOOLS inclusion levels and gene expression tables:
Import VAST-TOOLS’ output files (inclusion levels, cRPKMs and gene read count tables); in the visual interface, use the User-provided data loading panel and load a specific alternative splicing quantification or load the folder containing such file; in the command-line interface, use loadLocalFiles()
To parse splicing event from VAST-TOOLS in the command-line interface, use for instance parseSplicingEvent("HsaEX0007927", data=VASTTOOLSpsi)
Support for importing inclusion tables with arbitrary alternative splicing event identifiers (information for these events will not be available, such as event type and cognate gene)
SRA metadata:
Automatically load metadata from the SRA Run Selector (usually comes in files named SraRunTable.txt) avoiding the need to use prepareSRAmetadata() first
Alternative splicing diagrams now render automatically instead of showing SVG code (if printing more than one event, a table is displayed with event identifiers and respective diagrams)
Plot intron retention events (e.g. from VAST-TOOLS)
Alternative splicing quantification filtering (visual interface):
New panel to allow filtering already loaded alternative splicing quantification based on event types, samples, PSI statistics (such as median, variance and range) and cognate genes (some filtering steps may not be available when using user-provided tables with inclusion levels)
Filter data based on individual PSI values (also available when quantifying alternative splicing)
Filter VAST-TOOLS events based on its quality scores for read coverage
Toggle specific statistics based on alternative splicing quantification values when filtering
Preview the original and filtered events in an easy-to-use plot
Gene expression filtering:
Toggle specific statistics based on gene expression values when filtering (visual interface)
Tooltips of volcano plots now include diagram of alternative splicing events
Gene, transcript and protein annotation (visual interface):
Suggest genes based on loaded data
Change species and assembly when fetching information
Improve interface of PubMed article query, including persistent user-inputted tags even when changing selected gene
Improve relevance of results from PubMed articles
Much faster calculation of row/column-wise means, medians, variances and ranges (helpful for plotting statistics of large datasets)
Include Dockerfile to create Docker images based on code revisions
Bug fixes and minor changes
Progress bar is now animated as in previous versions
Data loading (visual interface):
Allow to discard selected files in file browser input elements
When creating groups by sample index/identifiers, suggest sample names not only obtained from sample information, but also from alternative splicing quantification and gene expression datasets
“Browse…” button now opens file browser to select folder where data is stored (as expected) in GTEx and SRA panels
Only pre-create groups of genes (based on literature-based gene lists) if at least one of its genes exists in any of the loaded datasets
Fix gene expression summary plots not showing in specific situations
Fix library size plot not working properly and causing rendering issues
Fix settings used to quantify alternative splicing not showing up
Show errors raised while reading a file (e.g. if file is too big for available memory)
Show alert if no GTEx data options are selected
Show filename of the file used to load gene expression and alternative splicing data from GTEx and SRA
Show helpful context messages in panel interfaces
Improve visual interface and minor copy-editing
Local data loading:
Support loading data from GTEx V8 or previous releases
Fix bad formatting of help tooltips when using shiny 1.4.0 or newer (visual interface)
Gene expression filtering:
Hide message regarding the usage of no design matrix
Alternative splicing annotation:
Try to load cached alternative splicing annotation if a timeout occurs
Include gene symbols in custom annotations if available
Account for possible filename changes when parsing annotations from VAST-TOOLS, rMATS, SUPPA and MISO
Alternative splicing event selection (visual interface):
Include loading indicator while searching for events
Decrease number of operations performed after selecting an event
Fix crash when changing to an alternative splicing quantification dataset without the selected splicing event
Allow to search using an event identifier directly
Show event identifier instead of prettier identifier to avoid confusion
Data grouping (visual interface):
Simplify group selection interface
Fix suggested attributes and index/identifiers in group creation not being cleared when changing to datasets where such data is unavailable (thus showing the attributes/index/identifiers of the previous dataset)
Show an alert when there is no data to create groups
Dimensionality reduction:
performPCA() and performICA() now directly raise errors (instead of simply capturing and returning them)
PCA: loading plots now show parsed information of events (cognate gene, event type and genomic position) if available
PCA: the correct splicing event is now selected when clicking on any loadings in the loadings plot (visual interface)
Differential analyses (visual interface):
Use group colours in density plots of differential expression table
Fix occasional crash when performing differential analyses with different number of groups during the same session
Tooltips of volcano plots are now properly positioned in high-resolution screens
The correct splicing event is now selected when clicking the density plots or survival curves in the table
When creating a group from differential splicing results, correctly set cognate genes of alternative splicing events