Joint host transcriptome and microbiome analysis from bulk RNA-seq data.
Documentation | Installation | Quick start | User guide | References
MTD Explorer is an open-source workflow for joint analysis of host transcriptome and microbiome/metatranscriptome signals from bulk RNA-seq data.
It builds upon the original MTD pipeline developed by Fei Wu, Yao-Zhong Liu, and Binhua Ling, and extends it with updated installation, host support, taxonomic exploration, functional profiling, reproducibility summaries, and documentation.
The original MTD pipeline should be cited when using MTD Explorer.
The full documentation is available here:
https://patrick-douglas.github.io/MTD-Explorer/
Start with:
MTD Explorer can generate outputs for:
- host transcriptome analysis;
- host differential expression;
- microbiome taxonomic profiling;
- taxonomic exploratory summaries;
- Krona and GraPhlAn visualizations;
- microbiome group comparisons;
- HUMAnN-derived functional profiling;
- GO and KEGG functional summaries;
- ssGSEA host gene-set activity analysis;
- HAllA host-microbiome association analysis;
- reproducibility and methods reporting.
MTD Explorer currently focuses on bulk RNA-seq host-microbiome analysis.
The single-cell workflow from the original MTD pipeline is not part of the current MTD Explorer scope, tests, or claims.
Clone the repository:
git clone https://github.com/patrick-douglas/MTD.git
cd MTDCheck the available command-line options:
bash MTD_explorer.sh --helpFor installation and database setup, use the documentation:
https://patrick-douglas.github.io/MTD-Explorer/getting-started/installation/
The documentation includes dedicated pages for major output folders:
- Output files
- Taxonomic exploratory outputs
- Taxonomic visualizations
- Host expression outputs
- Microbiome comparison outputs
- Functional profiling outputs
- ssGSEA outputs
- HAllA integration outputs
- Methods and reproducibility outputs
If you use MTD Explorer, cite the original MTD publication:
Wu, F., Liu, Y.-Z., & Ling, B. (2022). MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data. Briefings in Bioinformatics, 23(3), bbac111. https://doi.org/10.1093/bib/bbac111
Also cite the individual tools and databases used in your analysis. See:
https://patrick-douglas.github.io/MTD-Explorer/reference/
In particular, if GNU Parallel is used in work leading to publication, check the recommended citation with:
parallel --citationMTD Explorer is built upon the original MTD pipeline by Fei Wu, Yao-Zhong Liu, and Binhua Ling.
The original repository is available at:
https://github.com/FEI38750/MTD
Please see the repository license file for usage terms.