## psichomics 1.0.0 (5 Oct, 2016)

• First release of psichomics
• Quantify, analyse and visualise alternative splicing data

## psichomics 1.0.1 (1 Dec, 2016)

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

## psichomics 1.0.2 (3 Dec, 2016)

• Fix UTF-8 encoding in author list

## psichomics 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

## psichomics 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

## psichomics 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 cutoff and present p-value of selected PSI cutoff
• 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

## psichomics 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 cutoff 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()
• 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
• Survival analysis:
• Fix incorrect number of patients from the survival groups in the contextual information for the selected cutoff (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

## psichomics 1.0.7 (22 Jan, 2017)

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

## psichomics 1.0.8 (21 Feb, 2017)

• 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
• Minor UI improvements

## psichomics 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