Welcome to the rnaseqExplorer. This software is designed to help users easily upload and analyze RNA sequencing data. The application provides a user-friendly interface that allows you to visualize your data through various plots and explore the results in an intuitive way.

rnaseqExplorer provides functionalities for data analysis, including filtering, normalization, and understanding gene expression through visualizations like:

• 🎻 Violin plots
• 🗺️ Heatmaps
• 📈 PCA
• 🔍 Gene annotation

With its dynamic, interactive design, rnaseqExplorer is an essential tool for RNA-seq dataset analysis. It empowers bench biologists to conduct exploratory data analysis with ease, while delivering in-depth insights for seasoned data analysts. 💡

Getting Started

To use this application, clone the repository and follow the setup instructions in the documentation.

In R

You can install the package using the following command:

devtools::install_github("jeongahblairlee/rnaseqExplorer")
library(rnaseqExplorer)
launchApp()

If you want to try the example data:

devtools::install_github("jeongahblairlee/rnaseqExplorer")
library(rnaseqExplorer)

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("airway")
library(airway)
launchApp()

In web interface

You can also access the application via the web interface:

https://jeongahblairlee.shinyapps.io/rnaseqExplorer/ (currently sever is down)

Warning: In case the dataset is large, I recommend using R due to limitations from the web server.

Workflow

In the Workflow, you can see the overall workflow of the RNAseq Explorer application:

How to Use

Step 1: Upload Your Data

To get started, upload your RNA sequencing data using the provided functionality:

Step 2: Explore the Data

Once your data is uploaded, you can explore it through various visualization options:

2-1. Violin Plot

Generate violin plots to visualize the distribution of your data:

2-2. Heatmap

Create heatmaps for a detailed view of the gene expression levels:

2-3. PCA

Perform Principal Component Analysis (PCA) to understand the variance in your data:

Contributions

We welcome contributions to enhance the functionality and usability of RNAseq Explorer. Please feel free to submit a pull request or open an issue to discuss improvements.

License

This project is licensed under the GNU GENERAL PUBLIC LICENSE - see the LICENSE file for details.

Citation

If you use the rnaseqExplorer package in your research, please consider citing it as follows:

Jeongah Lee. (2024). rnaseqExplorer: A comprehensive Shiny application for analyzing RNA sequencing data (Version 0.1.0) [R package]. GitHub. https://github.com/jeongahblairlee/rnaseqExplorer

Contact

For any inquiries or issues, please contact Jeongah Lee.