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GTEx data can now be automatically downloaded and loaded on-demand
By default, data table now only displays at most the first 100 columns for performance reasons
Alternative splicing quantification:
Allow to discard samples before alternative splicing quantification
In alternative splicing quantification dataset summary, plot quantification based on median, variance and range per splicing event across samples to provide tools to filter quantification (plotRowStats())
Gene expression filtering and normalisation:
Allow to discard samples before filtering and normalisation
Filter low read counts using edgeR::filterByExpr()
Allow to perform limma::voom() on gene expression data (without design matrix) and to apply its normalisation methods
In gene expression dataset summary, plot distribution of gene expression per sample, distribution of library sizes and gene-wise mean and variance of gene expression across samples to provide the user tools to assess gene expression normalisation (plotGeneExprPerSample(), plotDistribution() and plotRowStats(), respectively)
Convert between different gene identifiers (the original identifier is kept in some conditions, read convertGeneIdentifiers()); in the visual interface, when filtering and normalising gene expression, ENSEMBL identifiers are converted to gene symbols, by default
Groups:
By default, load pre-made lists of genes when loading gene expression or loading/performing alternative splicing quantification
Added pre-made list of genes that encode for RNA-binding proteins (Sebestyen et al. 2016), useful to postulate about the regulatory role of those proteins based on gene expression and PSI correlation analyses
Correlation analyses:
Allow to use groups of genes and alternative splicing events in correlation analyses
Plot specific combinations of gene and alternative splicing events ([.GEandAScorrelation())
Display progress when performing correlation analyses
Display correlation results in a table (as.table())
Survival:
Render p-value plot by cutoff in command-line interface (plotSurvivalPvaluesByCutoff())
Gene, transcript and protein information:
Modify keywords used to search for PubMed articles
Bug fixes and minor changes
Improve console logging of error and warning alerts
Fix crash when loading psichomics with test data that is not locally available (by automatically downloading said data if not found)
Allow to edit file path in file/directory browser elements
Documentation:
Export functions mentioned in the documentation
Hide documentation of internal functions from the PDF reference manual
Loading SRA data:
Accept a vector of files as the first argument (easier to use with list.files())
Ask to overwrite file if one exists with the same name as the output file
Groups:
Automatically set dropdown width for group attribute selection
Minor improvements to the group creation interface
Fix error when creating groups containing only samples and no matching subjects
Fix warning when displaying group preview only based on subjects or samples
Alternative splicing quantification:
Automatically set the human genome version after loading data from TCGA (hg19), GTEx (hg19) or recount2 (hg38)
Fix progress bar
Decrease loading time after quantifying alternative splicing
By default, quantify skipped exons, mutually exclusive exons, alternative 3' and 5' splice sites, and alternative first and last exons; the default option is now consistent across both the visual and command-line interfaces)
Differential analyses:
Allow distribution plots to show the name of the samples when hovering or when a rug plot is rendered if rugLabels = TRUE (function plotDistribution())
Fix distribution plots requiring all samples in a group when using function plotDistribution()
Fix group colours and opacity for rug plot points within the distribution plot (occurred in the command-line version; function plotDistribution())
Fix wrong information in the table of differential splicing results (only occurs when the first splicing event is one for which there is not enough information to calculate statistical tests)
Fix inconsistency when presenting median and variance differences between gene expression and alternative splicing quantification
Fix error when groups contain samples outside the data being analysed
Gene, transcript and protein information:
Fix article title formatting (e.g. bold and italics)
Update psichomics citation with journal publication date