dorra28/AML-microbiome-chemotherapy: AML Microbiome Analysis Pipeline

This repository contains the complete computational analysis pipeline for investigating gut microbiome changes in acute myeloid leukemia (AML) patients before and after chemotherapy treatment. The analysis uses 16S rRNA sequencing data from 54 stool samples (22 pre-chemotherapy, 32 post-chemotherapy) retrieved from NCBI SRA (SRP141394). Key components: DADA2 pipeline for quality control and ASV inference Taxonomic classification using SILVA database v138 Alpha diversity (Shannon, Simpson) and beta diversity (Bray-Curtis) analyses Differential abundance testing with DESeq2 Functional prediction using PICRUSt2 Publication-ready visualization scripts Original data source: Rashidi et al. (2022), NCBI SRA SRP141394