We implemented the Gleesso pipeline to adapt the SPIEC-EASI pipeline to shotgun MGS abundances. From the Matrix of MGS abundance the pipeline goes through the following step:
- Select MGS that are present in at least 5% of samples and have a mean FPKM abundance of 10−7 across samples.
- Infer the graph with the SPIEC EASI pipeline.
- Infer the community structure with the walktrap algorithm from the igraph R package http: //igraph.org/r/.
- Output the graph structure to a Gephi https://gephi.org/ compatible format.
- Compute the community abundances by summing the abundance of MGS in the community.
The dependency packages phyloseq and SPIEC-EASI (https://github.com/zdk123/SpiecEasi) need to be manually installed before installing Gleesso.
The following code lines install both the dependencies and the gleesso package.
install.packages('devtools')
library(devtools)
source("https://bioconductor.org/biocLite.R")
biocLite("phyloseq")
install_github("zdk123/SpiecEasi")
library(SpiecEasi)
install_github("hjulienne/Gleesso_Pipeline/Gleesso")Consult the Gleesso walkthrough notebook :