Scripts and data related to the manuscript Uemura, Nakano, et. al, 2018
Here we provide the scripts that were employed to analyse and visualise the proteome data as presented in the manuscript Uemura, Nakano et al., 2018. The raw mass spectrometry data can be accessed at the ProteomeXchange Consortium via the PRIDE partner repository under the dataset identifier PXD009099.
The scripts necessary to reproduce the results and analyses reported in the paper can be found here:
SYP4 secretome scripts
Unprocessed raw data and intermediate results can be downloaded here:
SYP4 secretome data
Questions about the scripts and analyses can be addressed to Ryohei Thomas Nakano. For any general questions concerning the manuscript, please contact Prof. Paul Schulze-Lefert or Prof. Tomohiro Uemura.
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
Rhizobiales RNA-Seq scripts
Unprocessed raw data and intermediate results can be downloaded here:
Rhizobiales genomics dataset
Rhizobiales RNA-Seq dataset
Questions about the scripts and analyses can be addressed to Ruben Garrido-Oter or Ryohei Thomas Nakano. For any general questions concerning the manuscript, please contact Prof. Paul Schulze-Lefert.
R 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.
R scripts related to the manuscript by Dombrowski
et al., 2016
Here we provide the R scripts that were employed to analyse and visualise the sequencing data as presented in the manuscript Dombrowski et al. (2016), submitted to ISME. Raw sequencing reads were deposited at the NCBI Short Read Archive (SRA), BioProjectID PRJNA317760, accession number SRP073035.
The scripts used to analyze and generate the figures corresponding to the 16S data can be downloaded here:
Dombrowski et al. scripts
Questions about the scripts can be addressed to Dr. Nina Dombrowski. For any general questions concerning the manuscript, please contact Prof. Paul Schulze-Lefert.
R 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:
Bulgarelli et al. 16S scripts
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.
R 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.
Schlaeppi et al. R scripts
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.
R scripts related to the manuscript by Bulgarelli
et al., 2012
Below you can find custom R scripts that were specifically developed to analyze and visualize the sequencing data as presented in the figures of the article. We have documented the scripts to facilitate reproduction of main and supplementary figures.
Bulgarelli et al. scripts
In the zip file all scripts, functions and data files are included and organized in folders per figure. As a consequence, the same functions and data files can occur in multiple folders. The names of the tab-delimited data files in the figure folders correspond to sheet or file names in Supplementary Data 1 or 2 (which can be downloaded from nature.com).
The raw sequencing data has been deposited in the NCBI Short Read Archive (SRA043581). Questions for specific scripts can be addressed to the author indicated in the header of the script. For any general questions concerning the scripts, or the manuscript, please contact Prof. Paul Schulze-Lefert.