What is tmap?
For large scale and integrative microbiome research, it is expected to apply advanced data mining techniques in microbiome data analysis.
Topological data analysis (TDA) provides a promising technique for analyzing large scale complex data. The most popular Mapper algorithm is effective in distilling data-shape from high dimensional data, and provides a compressive network representation for pattern discovery and statistical analysis.
tmap is a topological data analysis framework implementing the TDA Mapper algorithm for population-scale microbiome data analysis. We developed tmap to enable easy adoption of TDA in microbiome data analysis pipeline, providing network-based statistical methods for enterotype analysis, driver species identification, and microbiome-wide association analysis of host meta-data.
How to Install?
To install tmap, run:
# (recommend) git clone https://github.com/GPZ-Bioinfo/tmap.git cd tmap python setup.py install # For some dependency problems. please install following packages. pip install scikit-bio R -e "install.packages('vegan',repo='http://cran.rstudio.com/')"
or you could also use pip now:
pip install tmap
After clone the repositories, you could use
cd tmap; docker build -t tmap .
If you encounter any error like
Import error: tkinter, you need to run
sudo apt install python-tk or
sudo apt install python3-tk.
- Basic Usage of tmap
- How to Choose Parameters in tmap
- Visualizing and Exploring TDA Network
- Network Statistical Analysis in tmap
- How tmap work
- Microbiome Examples
- Tutorial of executable scripts
For more convenient usage, we implement some executable scripts which will automatically build upon
$PATH. For more information about these scripts, you could see.
Tutorial of executable scripts
Liao, T., Wei, Y., Luo, M. et al. tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies. Genome Biol 20, 293 (2019) doi:10.1186/s13059-019-1871-4
If you have any questions or suggestions, you are welcome to contact us via email: email@example.com.