calour docs
2018.10.1
Site
General Calour concepts
Microbiome tutorials
Metabolome tutorials
Using Calour functions via the module and the Experiment class
Main classes and utility functions
Functions operating on
Experiment
object
Creating database interfaces for Calour
Page
Metabolome tutorials
Metabolome tutorials
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Example jupyter notebooks working with metabolome data
Calour mass-spec analysis demo
Using data from:
set up calour
Load MZmine2 feature table, metadata and GnPS file
Reorder the features (metabolites) and samples
Plotting the data
Differentially abundant metabolites between control (‘Air’) and treatment (‘IHH’) groups
Remove the age 10, 10.5 samples since very different from the rest
Find the differentially abundant metabolites
Plot these differentially abundant feature
Looking only at known metabolites
Differential abundance only on the identified metabolites
The metabolites higher in each group
Differentially abundant metabolites between baseline samples (age=10 weeks) and the rest
Metabolites higher in normal diet (10 weeks group)
Metabolites higher in high fat diet (>10 weeks group)
Looking at gnps components
Sorting by the cluster index
Merging all metabolites in each cluster
A code snipplet to add all gnps ids to each merged cluster
Now we can do this differential abundance analysis on these super-metabolites
Looking for metabolite artifacts
(split features due to RT/MZ tolerances during feature finding)
Similar mz and RT and same trend across samples
Identical m/z and very close RT
