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tmap

topological data analysis of population-scale microbiomes

https://github.com/gpz-bioinfo/tmap

Science Score: 13.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.8%) to scientific vocabulary

Keywords

microbiome-analysis topological-data-analysis
Last synced: 9 months ago · JSON representation

Repository

topological data analysis of population-scale microbiomes

Basic Info
  • Host: GitHub
  • Owner: GPZ-Bioinfo
  • License: gpl-3.0
  • Language: Python
  • Default Branch: master
  • Homepage: https://tmap.readthedocs.org
  • Size: 11.4 MB
Statistics
  • Stars: 31
  • Watchers: 1
  • Forks: 12
  • Open Issues: 1
  • Releases: 0
Topics
microbiome-analysis topological-data-analysis
Created almost 8 years ago · Last pushed over 3 years ago
Metadata Files
Readme License

README.md

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: bash # (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: bash pip install tmap

Now, we also provide a better way to install tmap package. Using docker and dockerfile to build a images to solve all dependency problems.

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.

Documentation

Quick Guides

You can read the Basic Usage of tmap for general use of tmap. Or follow the Microbiome examples for using tmap in microbiome analysis.

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

Publication

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

Contact Us

If you have any questions or suggestions, you are welcome to contact us via email: haokui.zhou@gmail.com.

Owner

  • Name: GPZ-Bioinfo
  • Login: GPZ-Bioinfo
  • Kind: organization

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 106
  • Total Committers: 6
  • Avg Commits per committer: 17.667
  • Development Distribution Score (DDS): 0.236
Top Committers
Name Email Commits
liaoth l****h@g****m 81
GPZ-Bioinfo 4****o@u****m 14
Cy l****c@f****m 7
GPZ-Bioinfo z****i@h****m 2
Channy 32bits 5****t@u****m 1
chenshuo c****n@1****m 1
Committer Domains (Top 20 + Academic)
163.com: 1 foxmail.com: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 5
  • Total pull requests: 13
  • Average time to close issues: 26 days
  • Average time to close pull requests: 4 days
  • Total issue authors: 5
  • Total pull request authors: 5
  • Average comments per issue: 2.4
  • Average comments per pull request: 0.0
  • Merged pull requests: 11
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ewancarr (1)
  • wyanren (1)
  • parsifal9 (1)
  • hellorp1990 (1)
  • bscully27 (1)
Pull Request Authors
  • 444thLiao (6)
  • lam-c (4)
  • GPZ-Bioinfo (1)
  • manto32bit (1)
  • CS0000 (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 531 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 6
  • Total maintainers: 1
pypi.org: tmap

A topological data analysis framework implementing the TDA Mapper algorithm for population-scale microbiome data analysis

  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 531 Last month
Rankings
Dependent repos count: 9.0%
Dependent packages count: 10.0%
Forks count: 10.9%
Average: 11.3%
Stargazers count: 11.7%
Downloads: 14.7%
Maintainers (1)
haokui
Last synced: 10 months ago

Dependencies

setup.py pypi
  • matplotlib >=2.2.2
  • matplotlib *
  • networkx ==2.2
  • numpy *
  • pandas >=0.23.0
  • plotly *
  • psutil *
  • rpy2 *
  • scikit-learn >=0.19.1
  • scipy *
  • statsmodels >=0.9.0
  • tqdm *
  • umap-learn *