1.4.0

• Support for loading new GTEx V7 data
• Support gene expression data:
  • Load, filter, normalise and perform log2-transformation on gene expression data
  • Perform principal component analysis based on gene expression data, survival analysis by gene expression cutoff and pairwise differential gene expression analysis
  • Correlate gene expression of a given gene against PSI values of multiple alternative splicing events
• Data loading:
  • Add step-wise instructions about loading of user-owned files
  • Filter GTEx junction quantification based on tissues of interest (all tissues are loaded by default)
  • Quantify splicing based on a list of genes (splicing events within all genes are quantified by default)
  • Parse sample information from TCGA samples using parseTcgaSampleInfo
  • Generate TCGA sample metadata when loading TCGA junction quantification
  • Present data summary after loading the data
• Data grouping:
  • Redesigned group creation and selection
  • Create groups based on genes and alternative splicing events
  • Assign a customisable colour per data group
  • Export or import patient and sample identifiers of data groups
  • Add new set operations when grouping (such as complement, subtraction and symmetric difference)
  • Suggest attributes of interest when creating groups
  • Allow to retrieve the universe of patient and sample identifiers by performing the complement group without any group selected
  • Statistically analyse group independence (useful to assess the overlap between a PCA cluster and groups derived from clinical and sample attributes, for instance)
• Differential analysis:
  • Label points based on top differentially spliced events or genes, selected alternative splicing events and/or selected genes
  • Create AS event and gene groups based on filtered or selected AS events and genes in the tables
• Dimensionality reduction techniques:
  • Subset data based on groups of AS events and genes before performing dimensionality reduction
  • Create data groups based on the partitioning clustering of PCA scores
  • Perform independent component analysis (ICA) on alternative splicing quantification and gene expression data
• Survival analysis:
  • Add p-value plot to visually infer the significance of survival analyses based on multiple alternative splicing quantification cutoffs
• Gene, transcript and protein information:
  • Information retrieval is now only dependent on a user-defined gene, instead of requiring alternative splicing quantification data to be loaded

Bug fixes and other improvements

• Show progress bar when running in the command-line interface
• Fix inconsistent browser history navigation
• Updated the CLI vignette with information on analysing gene expression data and a quick reference for functions
• Update minimum version required of shiny (1.0.3)
• Avoid replacing selected groups when manipulating new ones
• Differential splicing analysis:
  • Fix data not being rendered in the table when zooming in the plot after data transformation was applied
  • Return p-value of NA instead of 0 when the value of Fligner-Killeen's Test for Homogeneity of Variance is infinite
  • Discard value transformations that may return invalid data for the values chosen for the X and Y axes
  • Fix point that remains highlighted in the plot after deselecting the only selected row of the table
  • Improve readibility of plot's tooltip
  • Improve survival curves based on the optimal alternative splicing quantification cutoff:
    • Include the survival curve previews in 3 new columns within the differential splicing analyses table, instead of below that table; those columns consist of the survival curves, the optimal PSI cutoff and the respective log-rank test's p-value
    • Allow to use survival data when plotting and table sorting
    • Include the optimal PSI cutoff and the respective log-rank test's p-value in exported tables
    • Fix link to survival analyses using the previously calculated PSI cutoff
• Principal component analysis:
  • When clicking on a alternative splicing event in the loadings plot, the appropriate differential splicing analyses will now be automatically rendered with the respective options, as expected
• Survival analysis:
  • Properly set the title of survival curves based on the selected splicing event's quantification
  • Improve readability of Cox PH models
  • When performing survival analyses by alternative splicing cutoff, each patient is assigned the PSI value from the respective sample; for patients with more than one sample, the assigned sample is chosen based on the most frequent sample type across all patients (before, the first matched non-normal or non-control samples were used)
• Multiple other bug fixes and visual improvements

1.2.1

• Gene, protein and transcript information:
  • Fix missing file required for transcript plots
• Update command-line interface tutorial to render a transcript plot

1.2.0

• Gene, protein and transcript information:
  • Fix tooltip text presentation in transcript plot
  • Fix JavaScript issues when zooming the transcript plot
  • Fix error when plotting events associated with multiple genes
  • Fix error when plotting single-exon transcripts
  • Protein name, length and function are now presented when available
  • Improved general presentation of the information
• Differential splicing analyses:
  • Click and drag in the plot to zoom in and subsequently filter events
    shown in the table
  • Decreased step of sliders
  • Improve interface of previewed survival curves
  • When clicking on a table link to navigate to differential splicing
    analyses of a single event, the appropriate analyses will now be
    automatically rendered with the respective options, as expected
• Settings (renamed to "Help"):
  • Add links to tutorials and user feedback
  • Add app information and acknowledgments
  • Remove unused option for choosing cores (all performed operations are
    still single-core, given the difficulty of working with multiprocesses
    in Shiny)
• Improve dialogs regarding missing data and other minor interface elements
• Update documentation with volcano plot

1.1.9

• Differential splicing analyses:
  • Add volcano plot to represent events through selected attributes, such
    as p-values and descriptive statistics (e.g. median and variance)
    between groups of interest
  • Transform values of the X and Y axis in the plot using log
    transformed, inverted and absolute values, for instance
  • Highlight events in the plot based on values of the X and Y axis
  • Table of differential analyses per alternative splicing event is
    filtered according to highlighted and selected events in the plot
• Gene, protein and transcript information:
  • Transcript plot is now interactive and zoomable
  • Protein are now rendered based on selected transcript alone
  • Faster parsing of Uniprot's web API response
  • Improve display of article information when data is missing
• Principal component analysis:
  • Improve presentation of available options
• When clicking on previews of differential splicing and survival analyses,
  the appropriate analyses will now be automatically rendered with the
  respective options
• Fix buggy browser history when the user is directed to a different tab
• Consistently use Firebrowse and Firehose across the package
• Update documentation

1.0.8

• Support GTEx data loading and analysis
• Fix clinical data dependency:
  • Fix error when trying to load a file containing alternative splicing
    quantification without first loading clinical data
  • Fix error where samples from junction quantification were matched to
    clinical information even if clinical data were not loaded
  • Inform user when clinical data is not loaded while trying to plot
    survival curves
• Improve data grouping:
  • Create sample groups like patient groups and perform set operations
    between any created groups
  • Create groups using patient and sample identifiers
  • Check number of patients and samples per group
  • Rename selected groups
  • Alert user when groups cannot be created due to missing data
• Differential splicing analysis:
  • Analyse all samples as one group
• Survival analysis:
  • Select any clinical attribute for starting/follow up and ending times
• Create table containing TCGA sample metadata when calculating or loading
  alternative splicing quantification
• Minor UI improvements

1.0.7

• Survival analysis:
  • Fix error caused by some non-matched patients not being present in the patient-sample matching matrix

1.0.6

• Update tutorials with more relevant and complex examples
• Update minimum versions required of highcharter (0.5.0) and shiny (1.0.0):
  • Fix function usage as according to new version of highcharter
  • More options available when exporting plots (PNG, JPEG, SVG, XLS and
    CSV)
• Faster alternative splicing quantification
• Differential splicing analysis:
  • Fix major bug where samples could be placed in the wrong groups
  • Shorten speed of the calculation for the optimal PSI cut-off that
    minimises the survival difference
  • Fix not performing statistical tests for two selected sample types
    while analysing a single event with three or more sample types
  • Fix differential analysis on one splicing event not working when using
    diffAnalyses() function
  • Fix differential analysis not showing for individual events before
    navigating to the page where the analysis is performed for all events
  • Improve readability and information of statistical tests for single
    events
• Principal component analysis:
  • Shorten time taken to calculate principal components and to render the
    loadings plot
  • Fix loadings plot error when rendering some principal components
• Survival analysis:
  • Fix incorrect number of patients from the survival groups in the
    contextual information for the selected cut-off (below the slider)
  • Improve how alternative splicing quantification is assigned to
    patients based on their samples
• Protein annotation:
  • Warn user when trying to render proteins with no domains

1.0.5

• Navigate history using the browser forward and back buttons
• Fix delay when displaying large data by removing columns containing
  missing values exclusively
• Principal component analysis:
  • Improve speed when calculating total contribution of each variable to
    the principal components
• Survival analysis:
  • Shorten calculation of optimal PSI that minimises the survival
    difference
  • Improve visual cues of optimal PSI cut-off and present p-value of
    selected PSI cut-off
  • Fix ambiguous error messages
  • Fix incorrect Cox model results for formula-based calculations
  • Fix null Cox models crashing the program
• Differential splicing analysis:
  • Select sample types for differential splicing analysis
  • Fix statistical tests not displaying for individual events after
    differentially analysing all events using the other statistical tests

1.0.4

• Correctly load files and quantify alternative splicing for PRAD, OV and
  PAAD tumour types from The Cancer Genome Atlas (TCGA)
• Fix session disconnecting when exporting plots in Firefox
• Improve text and behaviour of fields to select datasets and AS events
• Fix author names and add contributor

1.0.3

• Bug fixes regarding gene annotation
:
  • Fix disabled gene selection when choosing a splicing event associated with a single gene after selecting an event related to multiple genes
  • Fix display of PubMed articles related to previously selected gene when selecting a single-gene-associated event after selecting an event related to multiple genes
• Bug fixes regarding groups:
  • Fix groups by rows not working
  • Fix group selection not working when only one group exists
  • Improve argument name of getGroupsFrom()
• Other minor improvements