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psichomics 1.8.1 (3 December, 2018)

  • Add tag ImmunoOncology to BiocViews

psichomics 1.8.2 (26 March, 2019)

  • Data loading:
    • 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:
  • 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

psichomics 1.8.3 (21 April, 2019)

Replace deprecated R.utils::evalWithTimeout() with R.utils::withTimeout()