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wkumler / MesoscopeMetabolomicsManuscript

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Report software version numbers #12

Closed wkumler closed 1 day ago

wkumler commented 4 days ago

Reviewer 2 | 04 Oct 2024 | 12:20 Software: Give the version number of the software used (e.g. Proteowizard, msConvert, XCMS...)

wkumler commented 1 day ago

Proteowizard: 3.0.19297 is currently installed on the lab computer but I don't remember if I redid the mzML conversion at some point Skyline: No idea. Was using Skyline when version 4.1 was out and my SkylineRunner executable is tagged as 21.2.0.470 so I guess I'll report both). Multiple version have definitely touched the files too. MSDIAL: Probably 4.36? Again, I likely used multiple versions and don't remember exactly which one was used for integration (possibly also multiple bc Laura and undergrads were working on this simultaneously but definitely v4) XCMS: 3.10.0 (was definitely using XCMS on this data at this time and don't thing I've rerun things since R: 4.4.0 (currently installed) vegan: 2.6-6.1 (currently installed)

I unfortunately haven't been great about dependency managing so the above are kinda just my best guesses. Not to mention that some files have been touched by multiple versions (e.g. reintegrating Skyline/MSDIAL) and I'm not sure which one is best to report. Not reporting Windows version (many) or any of the other million nuances that would make reproducibility guaranteed anyway.