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Expand Up @@ -55,7 +55,7 @@ We will update the citation guidelines as soon as the preprint is published.

## Important Note on CRAN Version {#cran-version-note}

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:
The `MicrobiomeStat` package is under continuous development. As a result, the most recent features have not yet been incorporated into the version available on the CRAN repository. The current CRAN version supports only the `linda` and `linda.plot` functions. For users who require a broader range of functionalities, especially those related to the analysis of longitudinal data, it is advisable to install the development version directly from GitHub. This process necessitates the prior installation of the `devtools` package.

```R
install.packages("devtools")
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# Online Tutorials {#online-tutorials}

`MicrobiomeStat` offers a **supportive toolkit** for microbiome data analysis, providing a range of capabilities from data input to visualization.
`MicrobiomeStat` provides a comprehensive suite of tools for microbiome data analysis, encompassing a variety of functions from data input to visualization.

To **familiarize** yourself with `MicrobiomeStat`, we invite you to explore our detailed online tutorial using GitBook. This tutorial includes:
To acquaint users with `MicrobiomeStat`, we offer an extensive online tutorial on GitBook. The tutorial covers the following areas:

- **Step-by-Step Installation and Configuration Guidance**
- Help ensure your setup is correct and optimized.
- **Analysis Walkthroughs Inspired by Real-World Cases**
- Gain practical insights and skills.
- **Hands-On Code Examples**
- Get acquainted with `MicrobiomeStat` coding practices.
- **Guides on Result Interpretation and Visualization**
- Learn to understand and present your data effectively.
- **Frequently Asked Questions**
- Quickly find answers to common queries.
- Installation and Configuration Instructions
- These guidelines help ensure that your setup is correctly configured and optimized.
- Analysis Demonstrations Based on Real-World Scenarios
- These demonstrations provide practical insights and skills.
- Code Examples for Practice
- These examples allow users to familiarize themselves with `MicrobiomeStat` coding practices.
- Guides for Interpreting Results and Creating Visualizations
- These guides help users understand and effectively present their data.
- Answers to Frequently Asked Questions
- This section provides quick solutions to common questions.

## Acquaint Yourself for a Seamless Experience

Expand All @@ -126,44 +126,44 @@ To better understand the capabilities of `MicrobiomeStat`, we have outlined its

We stand on the shoulders of giants with `MicrobiomeStat`, and our heartfelt gratitude goes out to the diligent and brilliant developers of the dependencies that our package relies on. Their remarkable efforts have not only made our work possible but have also significantly elevated the standards of computational tools available to the scientific community:

- **Core Dependencies:**
- Core Dependencies:
- R (>= 3.5.0), rlang, tibble
- **Imported Packages:**
- Imported Packages:
- ggplot2, matrixStats, lmerTest, foreach, modeest, vegan, dplyr, pheatmap, tidyr, ggh4x, ape, GUniFrac, scales, stringr, rmarkdown, knitr, pander, tinytex
- **Suggested Packages:**
- Suggested Packages:
- ggrepel, parallel, ggprism, aplot, philentropy, forcats, yaml, biomformat, Biostrings

Furthermore, we extend our deepest appreciation and respect to the trailblazers in the microbiome research community who have created and maintained the following remarkable tools. Their pioneering work has laid down paths through the complex landscape of microbiome data analysis, and we are truly honored to walk alongside:

- **microbiomeutilities**, **phyloseq**, **microbiomemarker**, **MicrobiomeAnalyst**, **microbiomeeco**, **EasyAmplicon**, **STAMP**, **qiime2**, and **MicrobiotaProcess**
- `microbiomeutilities`, `phyloseq`, `microbiomemarker`, `MicrobiomeAnalyst`, `microbiomeeco`, `EasyAmplicon`, `STAMP`, `qiime2`, and `MicrobiotaProcess`

Their contributions inspire us to continue improving and expanding the capabilities of `MicrobiomeStat`, and we sincerely hope our humble addition proves to be a useful complement to the incredible array of tools already available to researchers.

### User Support {#user-support}

`MicrobiomeStat` is designed with users in mind. Comprehensive [**documentation and tutorials**](https://www.microbiomestat.wiki/) are available to assist both novice and experienced researchers. Before posting a question or issue, we encourage users to [check previous questions and issues](https://github.com/cafferychen777/MicrobiomeStat/issues?q=is%3Aissue+is%3Aclosed) to see if the topic has already been addressed. If not, feel free to [open a new issue on GitHub](https://github.com/cafferychen777/MicrobiomeStat/issues). We are here to help you navigate any challenges you may encounter.
`MicrobiomeStat` is designed with users in mind. Comprehensive [documentation and tutorials](https://www.microbiomestat.wiki/) are available to assist both novice and experienced researchers. Before posting a question or issue, we encourage users to [check previous questions and issues](https://github.com/cafferychen777/MicrobiomeStat/issues?q=is%3Aissue+is%3Aclosed) to see if the topic has already been addressed. If not, feel free to [open a new issue on GitHub](https://github.com/cafferychen777/MicrobiomeStat/issues). We are here to help you navigate any challenges you may encounter.

### Ongoing Development {#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.
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 {#collaborative-development}

`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](https://github.com/cafferychen777/MicrobiomeStat/pulls) are welcomed**, and you can also share your ideas in the [**discussion area**](https://github.com/cafferychen777/MicrobiomeStat/discussions) of our GitHub repository. Engage with other community members and help us make `MicrobiomeStat` an even more useful tool for microbiome research.
`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](https://github.com/cafferychen777/MicrobiomeStat/pulls) are welcomed, and you can also share your ideas in the [discussion area](https://github.com/cafferychen777/MicrobiomeStat/discussions) of our GitHub repository. Engage with other community members and help us make `MicrobiomeStat` an even more useful tool for microbiome research.

### Conclusion {#conclusion}

`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.
`MicrobiomeStat` aims to serve as a dependable and efficient resource for microbiome data analysis. We extend an invitation to those who value open-source collaboration to join our community and contribute to its ongoing development.

| **Feature** | **Description** |
|------------------------------------|-----------------------------------------------------------------------------------------------------------------------|
| **[Data Import and Conversion](https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/laying-the-foundation-creating-the-microbiomestat-data-object)** | Supports numerous input formats from tools like **[QIIME2](https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/laying-the-foundation-creating-the-microbiomestat-data-object/importing-data-from-qiime2-into-microbiomestat), [Mothur](https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/laying-the-foundation-creating-the-microbiomestat-data-object/fetching-data-from-mothur-into-microbiomestat), [DADA2](https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/laying-the-foundation-creating-the-microbiomestat-data-object/integrating-data-from-dada2-into-microbiomestat), [Phyloseq](https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/laying-the-foundation-creating-the-microbiomestat-data-object/navigating-data-from-phyloseq-into-microbiomestat)** and more |
| **[Cross-sectional Study Analysis](https://www.microbiomestat.wiki/cross-sectional-study-design/unraveling-cross-sectional-studies-with-microbiomestat)** | Comprehensive analysis of **cross-sectional studies** |
| **[Paired Sample Analysis](https://www.microbiomestat.wiki/paired-samples-analysis/unveiling-paired-samples-analysis-a-comprehensive-guide)** | Tool for analyzing **paired samples** |
| **[Longitudinal Study Analysis](https://www.microbiomestat.wiki/longitudinal-study-design/grasping-longitudinal-studies-introduction-and-dataset-overview)** | Exploration of **temporal dynamics** of the microbiome |
| **Report Generation Functions** | Individual report functions for [**cross-sectional**](https://www.microbiomestat.wiki/cross-sectional-study-design/cross-sectional-reporting-microbial-analysis-reports-with-microbiomestat), [**paired**](https://www.microbiomestat.wiki/paired-samples-analysis/automated-reporting-for-paired-studies-microbiomestats-integrated-analysis-reports), [**longitudinal**](https://www.microbiomestat.wiki/longitudinal-study-design/longitudinal-reporting-microbiome-analysis-automation-with-microbiomestat) study designs. Shiny interface for one-click reporting is in development. |
| **Visualization Capabilities** | Wide variety of **visualization styles** |
| **Ongoing Development** | Continual **feature refinement** and **new functionality addition** |
| Feature | Description |
|--------------------------------|------------------------------------------------------------------------------------------------------------------|
| [Data Import and Conversion](https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/laying-the-foundation-creating-the-microbiomestat-data-object) | Accommodates multiple input formats from platforms such as [QIIME2](https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/laying-the-foundation-creating-the-microbiomestat-data-object/importing-data-from-qiime2-into-microbiomestat), [Mothur](https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/laying-the-foundation-creating-the-microbiomestat-data-object/fetching-data-from-mothur-into-microbiomestat), [DADA2](https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/laying-the-foundation-creating-the-microbiomestat-data-object/integrating-data-from-dada2-into-microbiomestat), [Phyloseq](https://www.microbiomestat.wiki/setting-up-microbiomestat-installation-and-data-preparation/laying-the-foundation-creating-the-microbiomestat-data-object/navigating-data-from-phyloseq-into-microbiomestat) and others. |
| [Cross-sectional Study Analysis](https://www.microbiomestat.wiki/cross-sectional-study-design/unraveling-cross-sectional-studies-with-microbiomestat) | Offers thorough analysis for cross-sectional studies. |
| [Paired Sample Analysis](https://www.microbiomestat.wiki/paired-samples-analysis/unveiling-paired-samples-analysis-a-comprehensive-guide) | Provides tools for paired samples analysis. |
| [Longitudinal Study Analysis](https://www.microbiomestat.wiki/longitudinal-study-design/grasping-longitudinal-studies-introduction-and-dataset-overview) | Facilitates exploration of the temporal dynamics of the microbiome. |
| Report Generation Functions | Includes individual report functions for [cross-sectional](https://www.microbiomestat.wiki/cross-sectional-study-design/cross-sectional-reporting-microbial-analysis-reports-with-microbiomestat), [paired](https://www.microbiomestat.wiki/paired-samples-analysis/automated-reporting-for-paired-studies-microbiomestats-integrated-analysis-reports), [longitudinal](https://www.microbiomestat.wiki/longitudinal-study-design/longitudinal-reporting-microbiome-analysis-automation-with-microbiomestat) study designs. Development of a Shiny interface for one-click reporting is underway. |
| Visualization Capabilities | Supports a broad range of visualization styles. |
| Ongoing Development | Committed to continuous refinement of existing features and addition of new functionalities.

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.

Expand Down Expand Up @@ -192,7 +192,7 @@ Join our Discord community to stay on top of the latest updates, developments, a

[Join the MicrobiomeStat Discord Server!](https://discord.gg/BfNvTJAt)

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!
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!

## Share and Connect {#share-and-connect}

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