Scripts and data related to the manuscript Duran, Flores-Uribe, et al., under preparation
Here, we provide the scripts that were employed to analyse and visualise the data presented in the manuscript Duran, Flores-Uribe, et al., currently under preparation. Raw 16S rRNA amplicon reads will be deposited in the European Nucleotide Archive (ENA) under the accession number PRJEB43117.
Questions about the scripts and analyses can be addressed to Dr. Ruben Garrido-Oter.
Scripts and data related to the manuscript Wippel, Tao, et al., in press
Here we provide the scripts that were employed to analyse and visualise the data presented in the manuscript Wippel, Tao, et al., currently under preparation. Raw 16S rRNA amplicon reads will be deposited in the European Nucleotide Archive (ENA) under the accession number PRJEB37695. Similarly, whole-genome and -transcriptome data of the Lj-SPHERE core collection will be uploaded to the same database with the accession number PRJEB37696.
The scripts used for the computational analyses described in this study can be found here:
Raw data and intermediate results can be downloaded here:
Arabidopsis and Lotus 16S rRNA NatCom and SynCom datasets
Lj-SPHERE whole genome sequencing dataset
Lotus and Arabidopsis transcriptome dataset
Questions about the scripts and analyses can be addressed to Dr. Ruben Garrido-Oter. For any general questions concerning the manuscript, please contact Dr. Simona Radutoiu, Prof. Paul Schulze-Lefert or Dr. Ruben Garrido-Oter.
Scripts and data related to the manuscript Garrido-Oter, Nakano, Dombrowski, et. al, 2018
Here we provide the scripts that were employed to analyse and visualise the sequencing data as presented in the manuscript Garrido-Oter, Nakano, Dombrowski, et al. Sequencing reads for the RNA-Seq experiments and whole-genome assemblies can be accessed at the European Nucleotide Archive (ENA) under the accession codes PRJEB27007 and PRJEB26998, respectivelly.
The scripts necessary to reproduce the results and analyses reported in the paper can be found here:
Rhizobiales comparative genomics scripts
Unprocessed raw data and intermediate results can be downloaded here:
Questions about the scripts and analyses can be addressed to Dr. Ruben Garrido-Oter or Dr. Ryohei Thomas Nakano. For any general questions concerning the manuscript, please contact Prof. Paul Schulze-Lefert.
Scripts related to the manuscript by Zgadzaj, Garrido-Oter et al., 2016
Here we provide the scripts that were employed to analyse and visualise the sequencing data as presented in the manuscript Zgadzaj, Garrido-Oter et al. (2016), published in PNAS.
All scripts necessary to reproduce all results and figures presented in the paper can be found here:
Lotus japonicus microbiota scripts
The unprocessed raw data can be downloaded here:
Lotus japonicus microbiota dataset
Questions about the scripts and analyses can be addressed to Ruben Garrido-Oter. For any general questions concerning the manuscript, please contact Dr. Simona Radutoiu or Prof. Paul Schulze-Lefert.
Scripts related to the manuscript by Bai et al., 2015
Here we provide the scripts that were employed to analyse and visualise the sequencing data as presented in the manuscript Bai et al. (2015), published in Nature.
The scripts used to analyze and generate the figures corresponding to the 16S data can be obtained here:
bacterial culture collections scripts
All raw data necessary to reproduce the results presented in the article, as well as intermediate results can be downloaded here:
bacterial culture collections dataset
Questions about the scripts can be addressed to Ruben Garrido-Oter. For any general questions concerning the manuscript, please contact Prof. Julia Vorholt or Prof. Paul Schulze-Lefert.
Scripts related to the manuscript by Hacquard et al., 2015
The R scripts used to produce the results and figures presented in the article can be found in the following repository:
https://github.com/garridoo/chommeta
For questions about the scripts please contact Ruben Garrido-Oter. For any general questions concerning the manuscript, please contact Prof. Paul Schulze-Lefert.
Scripts related to the manuscript by Bulgarelli et al., 2015
Here we provide the scripts that were specifically developed to analyse and visualise the sequencing data as presented in the figures of the article Bulgarelli et al. (2015) published in Cell Host and Microbe. The raw sequence reads were deposited in the European Nucleotide Archive database (accession no. PRJEB5860).
The scripts used to analyze and generate the figures corresponding to the 16S data can be downloaded here:
and those corresponding to the metagenome data can be found here:
https://github.com/hzi-bifo/BarleyMeta
Questions about specific scripts can be addressed to the author indicated in the header of the script. For any general questions concerning the manuscript, please contact Prof. Alice C. McHardy or Prof. Paul Schulze-Lefert.
Scripts related to the manuscript by Schlaeppi et al., 2013
Here we provide the QIIME and R scripts and Supplementary Datasets related to the manuscript Schlaeppi et al. (2014) in PNAS. The raw sequence reads were deposited in the European Nucleotide Archive database (accession no. PRJEB5058).
The archive 'Schlaeppi_et_al_QIIME_scripts.zip' comprises the scripts that were utilized to process and analyze the pyrosequencing reads in QIIME. The scripts contain the functions and parameters used, allowing the reproduction of the analysis.
Schlaeppi et al. QIIME scripts
The Supplementary Datasets S8, S9 and S10 present output files from the QIIME analysis that were utilized for downstream analysis in R.
Schlaeppi et al. supplementary datasets
The file 'Schlaeppi_et_al_R_scripts.zip' contains the R scripts that were developed to analyze the 16S rRNA gene profiling data as presented in the figures of the article. We have documented the scripts to facilitate the reproduction of the analysis.
Questions about specific scripts can be addressed to the author indicated in the header of the script. For any general questions concerning the manuscript, please contact Prof. Paul Schulze-Lefert.