Data analysis of 16S rRNA gene sequences and ARG & MGEs abundances (qPCR array) of Code river in Indonesia
Contents
This repository contains R code and data files from the study by S. Johanna Muurinen, Windi I. Muziasari, Jenni Hultman, Katariina Pärnänen, Vanny Narita, Christina Lyra, Lintang N. Fadlillah Ludhang P. Rizki, William Nurmi, James M. Tiedje, Iwan Dwiprahasto, Pramono Hadi and Marko Virta about the antibiotic resistance and river health.
Included files
SmartChipTM Real-Time PCR (Takara Bio) results (7 files): Ind1-2017.txt, Ind2-2017.txt, Ind3-2017.txt, Ind4-2017.txt, Ind5-2017.txt, Ind6-2017.txt, all_Ichips (Mean and sd calculted for each sample in R using text files)
Metadata for ARGs and MGEs: Ind_metadata.txt
ARG and MGE annotation file: Ind_assays.txt
16S rRNA gene sequencing results (OTU data table): otutable_indonesia.txt
Script for data analysis in R that uses all the files above: IndonesiaF.R