All software dependencies and operating systems using in ‘Microbiome convergence enables siderophore-secreting-rhizobacteria to improve iron nutrition and yield of peanut intercropped with maize’
This analysis require a standard computer with enough RAM to support the in-memory operations.
This analysis is supported for windows and Linux, tested on the following systems:
Windows: 10
Linux: Ubuntu 20.10
phyloseq=1.34.0 #microbiome analysis
stats=4.2.2 #stats package
car=3.1-1 #companion to applied regression
forecast=8.2.0 ##box-cox数据变换 Data transformation
ggpubr=0.4.0 #"ggplot2" based publication ready plots
agricolae=1.3-5 #statistical procedures for agricultural research
PMCMRplus=1.9.6 #calculate pairwise mutiple comparisons
rcompanion=2.4.21 #fucntions to support extension education proguram evaluaion
vegan=2.5-7 # community ecology package
psych=2.2.5 # correlation analysis
ggplot2=3.4.0 #作图 plot
ggpubr=0.5.0 #添加显著性标记, Add the significance marker
dplyr=2.3.0 #数据清洗，Data cleaning
plyr=1.8.8 #数据清洗，Data cleaning
reshaped2=1.4.4 #数据清洗，Data cleaning
ggthemes=4.2.4 #ggplot所用主题，Themes for ggplot2
readxl=1.4.1 #读入 excel, read excel files
ggsci=2.9 #配色，Themed color paletttes for "ggplto2"
showtext=0.9-5 #字体设置, font setting
extrafont=0.18 #Tools for using fonts
sysfonts=0.8.8 #加载系统字体，loading the system fonts into R
Cairo=1.6-0 #抗锯齿,anti-aliasing
ggtree=3.4.4 #visualization of tree and annotation data
stringr=1.5.0 #字符串处理string operations
amplicon=1.14.2 # statistic and visualization for microbiome data QIIME2=2021.8 #microbiome analysis
TBLASTN+=2.10.0 #Phylogenetic tree construction
MAFFT=7.487 #Multiple sequence alignment
IQ-TREE2=2.1.4-beta #phylogenetic inference