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1.0.7 Release
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@atc3 atc3 released this 25 Mar 19:26
· 111 commits to master since this release
v1.0.7
8856c9b

Thanks to everyone who gave us feedback on our first release. We've implemented the following changes. Please open an issue on GitHub or contact the developers if you are having trouble running the app, or if you have a feature request.

  • Patch (v1.0.7, 2019-03-25):

    • Fix bug in intersected peptides module

  • Patch (v1.0.6, 2019-03-18):

    • Fix double log transform in plot: MS1 intensity of ID'd ions
    • Add TMT Labelling efficiency modules to SCOPE tab (requires search with TMT as variable mod on lysine or n-terminus)
    • Fix crash where text sanitization was applying on tables/datatables that errored out during report rendering
    • Add check for pandoc on PATH before generating report

  • Patch (v1.0.5, 2019-03-06):

    • Add column aliasing for forwards/backwards compatibility with MaxQuant
    • Add correlation plot to SCOPE tab
    • Add MS1 intensities of intersected peptides plot
    • Fix various axis labels
    • Fix namespace scoping issues between dplyr/plyr libraries
    • Fix default bins args to histogram plots
    • Fix Windows paths crashing PDF report generation via. pdflatex
    • Fix merging parameters.txt files between different MaxQuant versions

  • Patch (v1.0.4, 2019-02-28):

    • add miscleavage table, total ID rate modules
    • add help messages for PEP, PIF sliders
    • fix misc. javascript errors
    • fix bug where allPeptides would get completely filtered out due to empty PIF column
    • fix error messages relating to "Calculate peak properties" in MaxQuant

  • Patch (v1.0.3, 2019-02-20):

    • various UI improvements
    • add automatic version checker
    • move input file selection to settings tab
    • fix bug where missing file would crash during import
    • fix bug where global.R would be sourced multiple times
    • fix bug where older version of folder_list.txt would crash app during launch
    • fix "ghost" file levels persisting after being filtered out
    • fix bug where extremely sparse data would result in incorrect parsing of certain columns

  • Patch (v1.0.2, 2019-02-04):

    • add more modules to peptide identification tab
    • add report plot width, plot height
    • add apply button to experiment format string
    • add string extraction pattern for experiment renaming
    • add more modules to the peptide identification tab
    • fix crash when generating a report with a datatable with missing data
    • add ability to run report generation inline with another R script, instead of forcing it to be run through the command line.
    • fix custom name vector for report generation

  • Hotfix (v1.0.1, 2019-01-31): Force R version >= 3.5.0 for pacman dependency, Fix add folders for Windows

Major Changes

  • Command-line report generation via. the do-ms_cmd.R script
  • Table, Datatable, and Text modules
  • Restructure tabs/modules in the filesystem
  • Add global application settings in settings.yaml
  • Robust file renaming with format string and editable table
  • Replace folder picker with path entry and options for adding subfolders
  • Add "Summary" tab, with experimental name mappings, search parameters, and more

Minor Changes

  • Switch to pacman for installing and loading dependencies
  • Replace all plyr code with dplyr equivalents, and remove plyr from dependencies
  • Simplify folder table UI
  • Replace experiments checkbox group with shinyWidgets picker
  • Add more and more descriptive error messages to various modules
  • Fix combining dataframes with different columns, by only taking the intersect of columns
  • Add knitr dependency for table printing in PDFs with kable()
  • Update documentation files
  • Add example modules for each module type
  • Add more visual customization of modules, with plot and box width/heights
  • Add table of contents to documentation tab
  • Add parameters.txt and summary.txt as importable files, and add custom parsing logic for those two
  • Add PIF threshold slider (PIF has to be above this value)
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