DO-MS 2.1.0

Fixed typos and modified FWHM plot be easier to interpret visually.

DO-MS 2.0.9

Added Chromatography plot for DIANN module. With further additions to come.

Loading report output from DIANN now uses Arrow to read in .parquet version of the report since report.tsv is now outdated. This also comes with an increase in the data loading speed.

v2.0.8

Added median lines and modified log scale for MS2/MS1 Ratio Plots.

v2.0.7

Fixed DO-MS not starting up due to code typo.
Changed Log10 to Log2 scale in ion sampling intersected and normalized plots.
Added a Ms2:Ms1 Ratio Plot for DIA-NN module.

v2.0.6

What's Changed

• v2.0.6 by @GeorgWa
• new Modules by @OrhunKok
• new modules by @Andrew-Leduc

Full Changelog: v2.0.5...v2.0.6

DO-MS 2.0.5 DIA Edition

Major Update:

• Support for multiple input formats
• DIA data visualization for DIA-NN results
• Supports the thermo Orbitrap and TimsTOF platform

DO-MS 1.0.10 ReRelease

Re-upload of DO-MS version 1.0.10

DO-MS 1.0.9 Release

Patch notes:

• Catch bad user input for command-line implementation earlier on
• Prevent crashes from incorrect user-inputted regexes
• Change TMT Reporter Ion Intensity distributions so that each experiment is plotted separately, instead of only plotting one
• Added "Early" and "Late" labels to Apex Offset plot
• Account for missing PEPs for fractional and total ID plots
• Adapt DART-ID modules for the latest version of DART-ID

1.0.8 Release

Thanks again for all of the helpful feedback on our previous release (v1.0.7). 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 (v1.0.8, 2019-04-25):

• Placed validate step before plotting to ensure that data frames without entries (either by deliberate input or filtration) generate more informative error messages
• Corrected the missed cleavage percentage calculation to display '0' instead of 'NA' in cases where no matching entries were found for a given missed cleavage category (0,1, or 2)
• Removed the Targeting Evaluation tab from display. We hope to release this module at a later date.
• Placed additional conditional statements in the fractional identification rate and total identification rate plots to prevent errors in cases where filtration removed all entries from the evidence data frame

1.0.7 Release

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.

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• 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

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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)