On the first day of the European Conference of Computational Biology in Turku, I had the opportunity to demonstrate the iSEEtree shiny app during the workshop on “Orchestrating Microbiome Analysis with Bioconductor”. It was a great chance to share my contributions to open software development!

eccb2024

iSEEtree is designed for the interactive exploration of hierarchical data, such as microbiome data. It is freely available on Bioconductor at this address.

You can give it a try in R as follows:

library(iSEEtree)
library(mia)
library(scater)

# Import TreeSE
data("Tengeler2020", package = "mia")
tse <- Tengeler2020

# Add relabundance assay
tse <- transformAssay(tse, method = "relabundance")

# Add reduced dimensions
tse <- runMDS(tse, assay.type = "relabundance")

# Launch iSEE
if (interactive()) {
  iSEE(tse)
}