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, single-end and paired-end workflows, taxonomic exploration, functional profiling, input provenance, reproducibility summaries, optional Slurm/HPC execution, pipeline benchmarking, and expanded 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:
- Installation
- Verify installation
- Quick start
- User guide
- HPC / Slurm execution
- Pipeline benchmarking
- Academic references
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-Explorer.git
cd MTD-ExplorerCheck 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.