1.2.1 (24 Apr, 2017)
====================

    * 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 (22 Apr, 2017)
====================

    * 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

1.0.9 (10 Apr, 2017)
====================

    * 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 (21 Feb, 2017)
====================

    * 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 (22 Jan, 2017)
====================

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

1.0.6 (17 Jan, 2017)
====================

    * 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 (7 Jan, 2017)
===================

    * 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 (18 Dec, 2016)
====================

    * 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 (13 Dec, 2016)
====================
    
    * 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

1.0.2 (3 Dec, 2016)
===================

    * Fix UTF-8 encoding in author list

1.0.1 (1 Dec, 2016)
===================

    * Improve metadata (title, description, authors and vignette titles)

1.0.0 (5 Oct, 2016)
===================
    
    * First release of psichomics
    * Quantify, analyse and visualise alternative splicing data
