Scripts of Garrido-Oter, Nakano, and Dombrowski et al., Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia, Cell Host&Microbe, 24(1), 155-167 (2018).
originally by Ryohei Thomas Nakano
These scripts are made available to facilitate reproducibility of our research. If you re-use any or part of this code, please reference with comments and cite our paper! Raw data and intermediate results necessary to run these scripts can be downloaded here.
Scripts used for processing data, creating the figures and performing the statistical analysis reported in the manuscript.
Bash script for RNAseq read processing and mapping.
R script for preparing read count table from mapped sequence reads.
R script for fitting read counts to a generalized linear model.
R script for selecting Differentially Expressed Genes based on Likelihood Ratio Test.
R script for converting normalized read counts to gene-wise median-centered Z scores.
R script for calculating the best number of clusters for k-means.
R script for k-mean clustering.
R script for drawing heatmaps using various values.
R script for performing enrichment analysis of k-means clusters for Gene Ontology categories.
R script for fitting read counts from Castrillo et al..
11_compare_response-129E_vs_flg22.R
R script to compare plant response to Rhizobium 129E colonization and a chronic exposure to the flg22 MAMP.
R script that contains parameters required for the other scripts.
For any questions regarding these scripts, please contact
Ryohei Thomas Nakano