1
OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL 2018
2
Introduction
2.1
Preparing for the course
2.2
Useful functions
3
Set-up and Pre-processing
3.1
Structure
3.2
Making a phyloseq object
3.3
Read input to phyloseq object
3.4
Read the tree file.
3.5
Merge into phyloseq object.
3.6
Read test data
3.7
Pre-processing data check
3.7.1
Sequencing depth
3.7.2
Distribution of OTUs
4
Alpha diversities
4.1
Equal sample sums
4.2
Diversities
4.2.1
Non-phylogenetic diversities
4.2.2
Phylogenetic diversity
5
Composition plots
5.1
Barplot counts
5.2
Barplot relative abundance
5.2.1
Barplot customize
5.3
Heatmaps
6
Beta diversity metrics
6.1
Phylogenetic beta-diversity metrics
6.1.1
Unweighted Unifrac
6.1.2
Weighted Unifrac
6.2
Population-level Density landscapes
6.3
PERMANOVA
6.4
Checking the homogeneity condition
7
Core microbiota
7.1
Core microbiota anlaysis
7.2
Core abundance and diversity
7.3
Core visualization
7.3.1
Core heatmaps
8
Inference of Microbial Ecological Networks
8.1
Prepare data for SpiecEasi
8.2
SPIEC-EASI network reconstruction
8.2.1
Prepare data for plotting
8.2.2
igraph network
8.2.3
Network plot
8.3
Network properties
8.3.1
Modularity in networks
8.3.2
Network plot
8.3.3
Good reads for ecological networks
OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL 2018
OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL 2018
Sudarshan A. Shetty, Leo Lahti, Gerben DA. Hermes
2018-05-07
1
OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL 2018
