LongTREC-LRGASP Platform

A comprehensive web platform for systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

Overview

The LongTREC-LRGASP Platform provides a collaborative environment for researchers to:

• Submit predictions for transcript identification and quantification.
• Access benchmark datasets tailored for RNA-seq evaluations.
• Participate in structured evaluation challenges.
• Compare results and metrics with other participants for enhanced insights.

Features

🏆 Challenge Management

The platform supports three distinct challenges in RNA-seq analysis:

1. Challenge 1: Reconstructing full-length transcripts.
2. Challenge 2: Quantifying transcript abundance.
3. Challenge 3: De novo transcript reconstruction.

📂 Data Access

Curated datasets include:

• Human (WTC11): Comprehensive transcriptomic data from the human WTC11 cell line.
• Mouse ES Cells: High-quality RNA-seq data for benchmarking.
• Manatee Leukocytes: Unique dataset for diverse transcriptomics evaluations.

⚙️ Automated Evaluation

Submissions are processed with real-time feedback, providing detailed performance metrics.

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Installation

1️⃣ Clone the Repository

git clone https://github.com/your-repo/LRGASP-Platform.git
cd LRGASP-Platform

2️⃣ Set Up a Virtual Environment

python -m venv venv
source venv/bin/activate  # For Linux/Mac
venv\Scripts\activate     # For Windows

3️⃣ Install Dependencies

pip install -r requirements.txt

4️⃣ Run the Development Server

flask run

Usage

• Register for an account via the platform's web interface.
• Browse available challenges and associated datasets.
• Submit predictions through the upload interface.
• Access automated evaluation results for real-time insights.

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Contributing

We welcome contributions to the LongTREC-LRGASP Platform. Please follow these steps:

1. Fork the repository and create a new branch for your feature (e.g. new benchmarking datasets, benchmarking matrices) or bug fix.
2. Commit and push your changes to your fork.
3. Submit a pull request for review.

LongTREC_LRGASP_Platform