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lemaslab / rump

A Reproducible Untargeted Metabolomics Data Processing Pipeline
MIT License
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Images #46

Open XinsongDu opened 4 years ago

XinsongDu commented 4 years ago

This issue includes all images that are used in the documentation

XinsongDu commented 4 years ago
Metabolomics_Pipeline_V6
XinsongDu commented 4 years ago

design_file_format

XinsongDu commented 4 years ago

mass_detection

XinsongDu commented 4 years ago

chromatogram_builder

XinsongDu commented 4 years ago

smoothing

XinsongDu commented 4 years ago

chromatogram_deconvolution

XinsongDu commented 4 years ago

isotupe_grouping

XinsongDu commented 4 years ago

group_aligner

XinsongDu commented 4 years ago

peak_finder

XinsongDu commented 4 years ago

duplicate_filter

XinsongDu commented 4 years ago

Open MZmine-2.53 batch mode

Screen Shot 2020-07-12 at 1 40 51 PM
XinsongDu commented 4 years ago

Add mass detection to batch queue.

Screen Shot 2020-07-12 at 1 54 26 PM
XinsongDu commented 4 years ago

default mass detection algorithm of RUMP is centroid, now change it to local maxima:

XinsongDu commented 4 years ago

Click OK and use "save..." button to save config file to your computer

Screen Shot 2020-07-12 at 1 59 55 PM
XinsongDu commented 4 years ago

Open saved config file, copy the mass detection module to clipboard

Screen Shot 2020-07-12 at 2 00 19 PM
XinsongDu commented 4 years ago

Open "rump/batchfile_generator_pos_253.py" and replace mass detection module with your new mass detection module by pasting from your clipboard

Screen Shot 2020-07-12 at 3 03 20 PM

1

XinsongDu commented 4 years ago

add "\n\" to the end of each line you copied, then the file will be like the following: 2

XinsongDu commented 4 years ago

Add "\" to quotes in your new mass detection module: 3

nishachachad commented 4 years ago

RUMP Logo