Code repository for Probiotic treatment induces sex-specific neuroprotection after traumatic brain injury in mice

This respository contains scripts used in the analysis of gut microbiomes related to TBI disease state and how probiotics may ameliorate rehabilitation.

Illumina V1-V3 16S sequencing data analysis performed using nf-core ampliseq.

The parameters used in the analysis can be found in the ampliseq.sh

Most of the data vizualization was performed in R using phyloseq and microViz.

Differential abundance analyses on microbial counts performed using ANCOMBC2.