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RaMS (development version)

RaMS 1.4.3 (patch)

• Added timezone support to metadata’s timestamps (mzML files are all UTC afaik)
• Fixed several bugs in the README and vignettes (it’s been a minute since I recompiled these!)
• Switched to canonical CRAN URLs
• Handling Suggested packages in the tests more carefully (removed bulk tidyverse call)

RaMS 1.4

• Added MS3 support to file reading and minification
  • MS3 data is not automatically requested with “everything” (the default) and must instead be added (e.g. grab_what=c("everything", "MS3"))
  • msdata$MS3 has an additional column (prepremz) corresponding to the MS1 trigger while the premz now corresponds to the immediately preceding MS2 m/z trigger.
• Added option to include polarity as a column per request from MetabolomicsWorkbench
  • Enable by setting incl_polarity = TRUE in grabMSdata()
  • Not enabled by default to preserve back-compatibility
  • Polarity is encoded as 1 for positive mode and -1 for negative mode
• Added function to edit the retention times of existing mzML/mzXML files (editMSfileRTs)
  • Still feels like it’s in development, would love feedback on Github
• Swapped out demo files to test incl_polarity and MS3 data
• Updated tests and minification vignette to reflect new demo files

RaMS 1.3.4

• Added OpenChrom reading support, credit to @ethanbass for the PR (#18 on Github)
• Added several convenience functions and useful documentation for each
  • qplotMS1data, a shortcut for the common ggplot2 call
  • mz_group(), a way to group raw MS1 data into m/z bins given a ppm error
  • trapz(), for integrating RT/intensity data into peak area
• Added new vignette with speed & size comparison to other packages and methods
• Updated vignettes

RaMS 1.3.1 (patch)

• Squashed a bunch of bugs around CRAN submission
• Changed where unit tests write to
• Improved unit test coverage
• Fixed broken URLs
• Added base64encoding to the package officially

RaMS 1.3.0

DAD and chromatogram handling

• Added support for DAD (diode array detection) data with grab_what = "DAD", credit to @ethanbass for the code
• Added support for precompiled chromatograms with grab_what = "chroms", credit to @ricardobachertdacunha for the proposal
  • Also enables MRM data support per Github issue #6
• Squashed some bugs

RaMS 1.2.0

The tmzML release

• Added tmzmlMaker, a function that converts mzML and mzXML files to the new tmzML file type
• Imported between() and %between% from data.table to avoid the extra library() call every time
• Squashed some bugs

RaMS 1.1.0

The minification release

• Added minifyMSdata, a function that shrinks MS files by excluding masses
• Restructured demo files using the new minify* functions to include more useful data
• Added prefilter argument to grabMSdata that drops masses below a user-provided intensity threshold
• Added quick-start poster to README.md
• Added grabAccessionData, a function that extracts arbitrary MS metadata by HUPO-PSI accession number
• Squashed some bugs

RaMS 1.0.0

The first CRAN release

• Enabled rtrange parameter for mzXML files
• All retention times are now converted to minutes rather than seconds
• Added several vignettes and switched back to knitr for PDF support, abandoning plotly things
  • RaMS and friends: some examples of moving data between R and other languages
  • Basic integrations: some rudimentary code that can be used to manually integrate peaks
• Streamlined README.md

RaMS 0.3.0

The documentation update

• Expanded documentation for individual functions, both exposed and unexposed
• Expanded README.md to include simpler demos and link to vignette
• Created vignette to demonstrate the nuances of RaMS
• Created tests to stabilize future package development
• Streamlined example mzML and mzXML files

RaMS 0.2.0

The user-friendly update

• Combined mzML and mzXML handling into one wrapper, grabMSdata, which also handles multiple files simultaneously
• Created README.md and included several demos of package functionality
• Added several “minified” mzML and mzXML files for demos and examples

RaMS 0.1.0

The first update

• Defined major functions, constructed package skeleton

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.