MicrobiomeStat: Comprehensive & Longitudinal Microbiome Analysis in R

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.

Citations

General Citation for MicrobiomeStat

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 = {www.microbiomestat.wiki},
}

Special Citation for linda and linda.plot Functions

If you are using linda or linda.plot functions, please cite the following paper:

Zhou, H., He, K., Chen, J. et al. LinDA: linear models for differential abundance analysis of microbiome compositional data. Genome Biol 23, 95 (2022). https://doi.org/10.1186/s13059-022-02655-5

We will update the citation guidelines as soon as the preprint is published.

Important Note on CRAN Version

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:

install.packages("devtools")

Once devtools is installed, you can install MicrobiomeStat from GitHub using the following command:

devtools::install_github("cafferychen777/MicrobiomeStat")

Table of Contents

1. Online Tutorials
2. Benefits of Using MicrobiomeStat
3. Key Features
4. Assistance & Contact Information
5. Join Our Discord Community
6. Share and Connect

Online Tutorials

MicrobiomeStat represents a comprehensive toolset for microbiome data analysis, boasting extensive capabilities from data input to visualization.

For an in-depth understanding of MicrobiomeStat, we have curated a comprehensive online tutorial using GitBook, encompassing:

• Comprehensive installation and configuration guidance

• Analysis walkthroughs driven by real-world cases

• Hands-on code examples

• Detailed guides on result interpretation and visualization

• Frequently Asked Questions

For a seamless experience with MicrobiomeStat, we recommend acquainting yourself with these online tutorials:

MicrobiomeStat Tutorials: https://www.microbiomestat.wiki

Benefits of Using MicrobiomeStat

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.

Comparative Overview

For a thorough understanding of how MicrobiomeStat measures against other tools, we’ve provided detailed comparisons on our website:

• Comparison with Other Longitudinal Packages

• Comparison with Integrated Analysis Packages

User Support

MicrobiomeStat is designed with users in mind. Comprehensive documentation and tutorials are available to assist both novice and experienced researchers.

Ongoing Development

Ensuring that MicrobiomeStat remains a leading tool in its category requires ongoing development. We’re dedicated to regular updates and addressing user feedback.

Collaborative Development

MicrobiomeStat is an open-source tool, and we value contributions from the community. If you have suggestions or improvements, pull requests are welcomed.

Conclusion

MicrobiomeStat aims to be a reliable and efficient tool for microbiome data analysis. For those who value open-source collaboration, we invite you to be part of our community and contribute to its continuous improvement.

Key Features

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
Visualization Capabilities	Offers a wide variety of visualization styles
Data Export	Supports export of analysis results in diverse formats
Ongoing Development	Continual feature refinement and new functionality addition

Assistance & Contact Information

For assistance or inquiries, feel free to reach out to:

Name	Email
Dr. Jun Chen	[email protected]
Chen Yang	[email protected]

Engage in Our Discord Community

Join our Discord community to stay abreast of the latest developments in MicrobiomeStat, engage in discussions, and avail support:

Join the MicrobiomeStat Discord Server!

Our active community fosters an environment of collaboration, feedback, and continuous learning.

Share and Connect

Spread the word about MicrobiomeStat and stay connected through various platforms!