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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
    • 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 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)

  • 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

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