16S downstream analysis in Colorectal Carcinoma I Study Design and Data Norm (2 of 5)

#microbiome #bioinformatics #stackbarplots #beginners
Step2: Study design, data norm, top abundant taxa stack bars
Tutorial for comparing microbial communities between groups (alpha and beta diversity, DA taxa, co-abundance networks with species) when correcting for paired design in all of the above. This tutorial is suitable to run for data that has been generated with either 16S amplicon sequencing or shotgun metagenome sequencing.
There are valuable tips and tricks included in the analyses that are often difficult to find elsewhere.

htm file with R script and expected output:
https://rpubs.com/malina_19/1181149

Github repo:
https://github.com/malina-dva/16S-dow...

The role of the human microbiome in health and disease
   • The role of the human microbiome in health...  

Tutorial for Estimation of relative abundance of species in metagenome data
   • Estimation of relative abundance of specie...  

Tutorial for building co-expression network from gene expression data
   • Network generation  

Chapters:
00:00 Intro
00:01 Experimental design
02:52 Research questions to be addressed
06:05 R tutorial start (requirements) (better to run at speed of 1.25 from here)
08:05 Description of the data
12:45 Function to create phyloseq object from your own data
13:33 Data normalizations
15:58 Convert to rel abund
18:04 CSS normalization
19:08 CPM normalization
20:16 Rarefaction normalization
(Rarefaction video explanation    • How to find the best sampling depth for ra...  )
22:20 Plotting the top 15 taxa based on abund
22:47 Agglomerating the counts on the level of Genus
24:34 Plot top 15 Genera derived from CSS norm phyloseq object
29:20 Plot the Genera in individual facets
30:24 Plot top 15 Genera derived from TSS norm phyloseq object

Disclaimer
This tutorial is based on publicly available resources and my own understanding of 16S rRNA data analysis. The content presented here is for educational purposes only. Any opinions expressed are my own and do not represent the views of my employer. For detailed guidance, please refer to the original sources cited.

Main sources used for preparation of the videos:
Phyloseq, vegan, microbiomeMarker R vignettes were mainly utilized for the preparation of first three chapters (from 2 to 4 in the playlist).
Igraph R package and vignette were utilized for building the co-abundance networks.

#16SrRNA #phyloseq #metagenome #bioinformatics #16SrRNAdownstreamanalyses #shotgunsequencingdownstreamanalyses

#microbiome #bioinformatics #stackbarplots #beginners #R #microbiomeasy #shotgunsequencing #microbiomeMarker #stackbarplots #relativeabundance