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psichomics 1.6.1 (5 July, 2018)

  • Improve support for analysing SRA and user-provided data:
    • New tutorial on performing alternative splicing analysis using SRA and user-provided data from FASTQ files (other tutorials were also updated)
    • Process gene and splice junction counts from STAR output for subsequent loading into psichomics
    • Automatically download and load data from select SRA projects using the recount R package
  • Data grouping:
    • Preview groups based on selected attribute before creation
  • Gene, transcript and protein information:
    • Display alternative splicing events in transcript plot
  • Correlation between gene expression and alternative splicing:
    • Allow to change plot height and font size

Bug fixes and minor changes

  • Support new version of Human (hg38 assembly) alternative splicing annotation (fixes wrong coordinates for many minus-strand splicing events)
  • Fix issues with TCGA sample metadata:
    • No sample metadata loaded when loading TCGA files from local folder
    • Not retrieving sample metadata for all TCGA samples when multiple junction quantification files are loaded
  • Data grouping:
    • Correctly suggest how to select variables in subset expression and give more examples on how to use this feature
    • Fix subject/sample attributes not being updated for selection for the GREP interface
    • Fix error alerts not appearing when trying to create groups based on invalid parameters
    • Add an error alert when trying to extract group data from an user-provided file without such information
  • Alternative splicing quantification:
    • Fix crash when quantifying splicing for a single sample
  • Differential splicing analysis (exploratory):
    • Fix crash when inputting non-numeric values or minimum larger than the maximum limit as the axes for the splicing scatter plot

psichomics 1.6.2 (2 October, 2018)

  • Update citations to link to article in Nucleic Acids Research: https://doi.org/10.1093/nar/gky888
  • Copy-edit README, tutorials, DESCRIPTION, NEWS and code
  • Update screen shot
  • Add metadata regarding loaded datasets (for instance, path and name of files used for dataset loading, options set upon dataset creation, etc.)
  • Differential splicing and expression analysis:
    • Allow to input formulas when highlighting points; this is an improvement when plotting -log10(q-values), for instance, where it is now possible to highlight values >= -log10(0.05), i.e. q-values <= 0.5, instead of inputting an approximate value
  • Correlation analyses:
    • Colour samples by group
    • Render contour based on a density estimate
    • Display exportable table with correlation analyses
  • Groups:
    • Show group colour in group selection element
  • Retrieve articles from PubMed instead of PMC

Bug fixes and minor changes

  • Improve file browser input in remote servers:
    • Allow to directly input a path without using the file browser dialog
    • Display warning when calling the file browser dialog in RStudio Server or in an unsupported system
  • TCGA data:
    • Inform of sequencing technology used to obtain gene expression data
  • GTEx data:
    • Fix issues in downstream analyses when using GTEx data subset by tissues
  • Differential analysis:
    • Avoid limiting X axis of density plot when values outside 0 and 1 are provided, as in the case of gene expression (plotDistribution() function)
    • Fix filenames of exported tables from differential expression analysis incorrectly mentioning differential splicing analysis instead
  • Correlation analysis:
    • When plotting correlation analysis, loess curve was performed based on gaussian fitting, independent of the “family” argument of plotCorrelation()
  • Improve console logging of error and warning messages