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