Name		Name	Last commit message	Last commit date
data		data
pdf		pdf
16S.Rmd		16S.Rmd
README.md		README.md
bulk_rnaseq.Rmd		bulk_rnaseq.Rmd
humann.ipynb		humann.ipynb
kraken.Rmd		kraken.Rmd

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Microbiome (and microbiome-adjacent) analysis

This repo contains semi-generic R notebooks for analyzing microbiome (and microbiome-adjacent) data.

Analysis of bulk RNAseq data using DESeq2
Analysis of 16S counts produced by QIIME2
Analysis of shotgun metagenomic data produced by Kraken2

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Scripts for analyzing microbiome (and microbiome-adjacent) data

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