AlpineStreamMicrobiome

Alpine Stream Insect Microbiome Full Text: https://link.springer.com/article/10.1007/s10750-019-04097-w

Code files:

ItalyInvertRmarkdownJune8.rmd contains code used for in-text statistics and tables as well as data exploration

ManuscriptFigures.r contains code used in creating figures for manuscript

Data files:

ItalyInvert2018WTax.biom contain the filtered ESV abundances and taxonomy after filtering in QIIME 2

ItalyInvert11.29.18 contains an unrooted tree created using default settings in QIIME 2

ItalyInvertMetadataWDiversity3.5.2019.csv contains sample metadata as well as Shannon and Faith's PD computed in QIIME 2

ItalyInvertPiRUST2.20.19.biom contains PICRUST data (computed using QIIME 2 Plugin)

Output files

Figures/ Contains manuscript figures

ItalyInvertRmarkdownJune8.html contains results and figures used for data exploration, tables, and intext statistics

PhylumlevelRelAbu.csv Phylum level Relative bacterial abundance split by sample location and insect species

FamilylevelRelAbu.csv Family level Relative bacterial abundance split by sample location and insect species

see also: https://benbowlab.github.io/ItalyWorkshop.html