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glasgowcompbio / vimms

A programmable and modular LC/MS simulator in Python
MIT License
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Add peak only and XCMS to sequence manager #34

Closed vinnydavies closed 4 years ago

vinnydavies commented 4 years ago

Once we have the peak only (Simon) and XCMS (Ronan) peak picking methods set up to work within the ViMMS / Python framework, it would be good to add them (Vinny) to the sequence manager

joewandy commented 4 years ago

how's the peak picking results from peakonly? is it good?

sdrogers commented 4 years ago

it's fast, and looks ok Really easy to run (their latest release has a GUI). Open an .mzML, click "pick peaks", wait a minute or so...

joewandy commented 4 years ago

Not having a good peak picking method is the main thing that prevented us from creating a decent xcms-alternative in Python, right? So now it's all there.

sdrogers commented 4 years ago

Yes, possibly. Good point. Probably needs someone who knows that they’re on about to look at the output though...

Simon Rogers simon.d.rogers@gmail.com

On 17 Jul 2020, at 14:08, Joe Wandy notifications@github.com wrote:

Not having a good peak picking method is the main thing that prevented us from creating a decent xcms-alternative in Python, right? So now it's all there.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/sdrogers/vimms/issues/34#issuecomment-660097100, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAEVKY3WDYYBH2H24NAO2BLR4BEMVANCNFSM4O6HBBLA.

joewandy commented 4 years ago

Another question that came up in meeting: if we pass peakonly a partial chromatogram, could it still identify that it's a peak or not?

joewandy commented 4 years ago

To be discussed in issue #39