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IMAP:
Integrated Microbiome Analysis Pipelines
:
End-to-End Practical User Guides Using Integrated Approaches
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Table of contents
IMAP-Part 07: Microbiome Data Preparation Guide
GETTING STARTED
Preparing for Downstream Analysis
1
Data Tidying
MOTHUR OUTPUT
2
Prepare Mothur Output
QIIME2 OUTPUT
3
Prepare Qiime2 Output
PHYLOSEQ OBJECTS
4
Creating phyloseq Objects
EXTERNAL DATASETS
5
Phyloseq Objects Demo Datasets
PHYLOSEQ FUNCTIONS
6
Reviewing Phyloseq Objects
PHYLOSEQ EXTRA OBJECTS
7
Create psExtra Objects
CLEANING PHYLOSEQ OBJECT
8
Pipeline for Cleaning Phyloseq Objects
DATA TRANSFORMATION
9
Data Tranformation from Phyloseq Objects
DISTANCES MATRICES
10
Distance Calculation in Microbiome Data Analysis
11
What’s Next: Utilizing Transformed Data
DIMENSIONALITY REDUCTION
12
Dimensionality Reduction Techniques
13
Taxa Prevalence and Detection
APPENDIX
A
IMAP GitHub Repos
B
Session Information
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References
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Session Information
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