A repository for scripts from the manuscript "Repeated introduction of micropollutants enhances microbial succession despite stable degradation patterns"
by Dandan Izabel-Shen, Shuang Li, Tingwei Luo, Jianjun Wang, Yan Li, Qian Sun, Chang-Ping Yu, Anyi Hu*
Corresponding author: Dr. Anyi Hu, CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China; email: ayhu@iue.ac.cn
This work is currently Under Review. A preprint of this work can be found at DOI: 10.1101/2021.08.24.457489
##Data The sequencing data were deposited in the NCBI SRA database with the Bioproject number PRJNA497759. The codes are citable using https://doi.org/10.5281/zenodo.5242686
#The following packages (and their dependencies) are required to run the whole analysis
library("vegan"); packageVersion("vegan") # 2.5.6 library("phyloseq"); packageVersion("phyloseq") # 1.30.0 library("doParallel"); packageVersion("doParallel") # 1.0.15 library("foreach"); packageVersion("foreach") # 1.5.0 library("DESeq2"); packageVersion("DESeq2") # 1.26.0 library("ggplot2"); packageVersion("ggplot2") # 3.3.2 library("BiocManager"); packageVersion("BiocManager") # 1.30.10" library("gplots"); packageVersion("gplots") # 3. 1. 0 library("gridExtra");packageVersion("gridExtra") # 2.3 library("picante");packageVersion("picante") # 1.8.2 library("dplyr");packageVersion("dplyr") # 1.0.2 library("stats");packageVersion("stats") # 3.6.2 library("RColorBrewer");packageVersion("RColorBrewer") # 1.1.2 library("VennDiagram"); packageVersion("VennDiagram") # 1.6.20 library("ggpubr"); packageVersion("ggpubr") # 0.4.0 library("tidyverse"); packageVersion("tidyverse") # 1.3.0 library("car"); packageVersion("car") # 3.0.10 library("agricolae"); packageVersion("agricolae") # 1.3.3 library("scales"); packageVersion("scales") # 1.1.1. library("graphics"); packageVersion("graphics") # 3.6.0
## How to run
The R scripts in the base folder should be run interactively (for instance with RStudio).