sinCellTe 2024: scRNA-seq long reads analysis

Welcome to the sinCellTe 2024 practical session on single-cell RNA sequencing (scRNA-seq) analysis with long reads. This course is split into two main parts, each contained in separate R Markdown files that guide you through the process of preprocessing scRNA-seq isoform datasets and performing differential isoform expression analysis.

Course Structure

• scRNAseq_long_read_part_1.Rmd: Introduces the preprocessing of scRNA-seq isoform datasets. This part covers the creation of a multi-Assay Seurat object which consolidates various data types and preprocessing steps into a structured format suitable for downstream analysis.

• scRNAseq_long_read_part_2.Rmd: Uses the Seurat object created in Part 1 to conduct differential isoform expression analysis. This session aims to identify key differences in isoform usage between different cell types, providing insights into cellular functions and behaviors.

Repository Organization

.
├── data/                  # Datasets used in the analyses
├── imports/               # Additional scripts
├── LICENSE                # License details for the repository
├── README.md              # Overview
├── scRNAseq_long_read_part_1.Rmd  # R Markdown file for Part 1
├── scRNAseq_long_read_part_1.html # Compiled HTML from Part 1 R Markdown
├── scRNAseq_long_read_part_2.Rmd  # R Markdown file for Part 2
└── scRNAseq_long_read_part_2.html # Compiled HTML from Part 2 R Markdown

Getting Started

To get started with the practical sessions:

1. Clone the repository to your local machine.
2. Ensure you have R and the necessary packages installed.
3. Open the .Rmd files in RStudio to view and run the code.

Feel free to explore the data and scripts provided to enhance your understanding of scRNA-seq analysis with long reads.