The MicrobiomeStat package is a state-of-the-art R tool
with a special focus on the analysis of longitudinal microbiome
data. While capable of handling multi-omics data and
cross-sectional studies, its core strength lies in its
proficiency in longitudinal analysis. This makes it an
invaluable resource for researchers conducting extensive biological
studies over time.
If you are using features beyond the linda and
linda.plot functions, please cite as follows, until a
preprint version is published:
@Manual{,
title = {MicrobiomeStat: Comprehensive Statistical and Visualization Methods for Microbiome and Multi-Omics Data},
author = {Xianyang Zhang and Jun Chen and Caffery(Chen) Yang},
year = {2023},
note = {R package version 1.1.1},
url = {https://www.microbiomestat.wiki},
}MicrobiomeStat FunctionsIf you are using the linda, linda.plot,
generate_taxa_association_test_long,
generate_taxa_test_pair,
generate_taxa_test_single, or
generate_taxa_trend_test_long functions, please cite the
following paper:
@article{zhou2022linda,
title={LinDA: linear models for differential abundance analysis of microbiome compositional data},
author={Zhou, Huijuan and He, Kejun and Chen, Jun and Zhang, Xianyang},
journal={Genome biology},
volume={23},
number={1},
pages={1--23},
year={2022},
publisher={BioMed Central}
}We will update the citation guidelines as soon as the preprint is published.
Due to the ongoing development cycle, the
most up-to-date features of MicrobiomeStat
have not yet been uploaded to the CRAN repository. The
current CRAN version only supports the linda and
linda.plot functions. If you require
additional functionalities, particularly for analyzing
longitudinal data, we recommend installing the
development version from GitHub. To do this, you’ll first need
to install the devtools package if you
haven’t already:
Once devtools is installed, you can install
MicrobiomeStat from GitHub using the following command:
MicrobiomeStat represents a comprehensive
toolset for microbiome data analysis, boasting extensive
capabilities from data input to visualization.
For an in-depth understanding of
MicrobiomeStat, explore our detailed online tutorial using
GitBook. This tutorial covers:
MicrobiomeStat coding
practices.For a seamless experience with MicrobiomeStat, make the
most of these enriching resources:
📘 Explore MicrobiomeStat Tutorials
The field of microbiome research is complex and rapidly evolving. The
analytical tools chosen can have significant implications for research
outcomes. In this context, MicrobiomeStat presents itself
as a robust option.
For a thorough understanding of how MicrobiomeStat
measures against other tools, we’ve provided detailed comparisons on our
website:
MicrobiomeStat is designed with users in mind.
Comprehensive documentation and
tutorials are available to assist both novice and
experienced researchers. Before posting a question or issue, we
encourage users to check
previous questions and issues to see if the topic has already been
addressed. If not, feel free to open a
new issue on GitHub. We are here to help you navigate any challenges
you may encounter.
Ensuring that MicrobiomeStat remains a leading tool in
its category requires ongoing development. We’re
dedicated to regular updates and addressing user feedback.
MicrobiomeStat is an open-source tool, and we highly
value contributions from the community. If you have suggestions,
improvements, or feedback for future development directions and feature
additions, pull
requests are welcomed, and you can also share your ideas in
the discussion
area of our GitHub repository. Engage with other community
members and help us make MicrobiomeStat an even more useful
tool for microbiome research.
MicrobiomeStat aspires to be a reliable and
efficient tool for microbiome data analysis. For those who
cherish open-source collaboration, we warmly invite you
to join our community and contribute to its continuous enhancement.
| Feature | Description |
|---|---|
| Data Import and Conversion | Supports numerous input formats from popular tools like QIIME2, Mothur, DADA2, Phyloseq and more |
| Cross-sectional Study Analysis | Performs comprehensive analysis of cross-sectional studies |
| Paired Sample Analysis | Excellent tool for analyzing paired samples |
| Longitudinal Study Analysis | Allows for exploring the temporal dynamics of the microbiome |
| One-Click Report Generation | Generates professional analysis reports with a single click for cross-sectional, paired, longitudinal study designs |
| Visualization Capabilities | Offers a wide variety of visualization styles |
| Ongoing Development | Continual feature refinement and new functionality addition |
This approach ensures that users can effortlessly navigate to the
specific sections of the MicrobiomeStat documentation,
garnering detailed information and guidelines for diverse analysis
types. The structure and accessibility assist users in leveraging
MicrobiomeStat effectively for their microbiome data
analysis needs.
For those interested in seeing MicrobiomeStat in action,
we have prepared demo reports tailored to different study designs:
We encourage you to explore these examples and discover the powerful capabilities of our tool.
For assistance or inquiries, feel free to reach out to:
| Name | |
|---|---|
| Dr. Jun Chen | Chen.Jun2@mayo.edu |
| Chen Yang | cafferychen7850@gmail.com |
Join our Discord community to stay on top of the latest updates,
developments, and enhancements in MicrobiomeStat. Be part
of vibrant discussions, ask questions, share insights, and avail support
from peers and experts alike:
Join the MicrobiomeStat Discord Server!
In our Discord server, an automated bot keeps you informed about every package and tutorial update, ensuring you never miss out on new features, improvements, and learning materials. Our active community thrives on collaboration, feedback, and continuous learning, making it an invaluable space for both novice and experienced researchers navigating the world of microbiome data analysis. Stay connected, stay informed, and let’s advance the field of microbiome data analysis together!
Spread the word about MicrobiomeStat and stay connected
through various platforms!
