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README.md

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-# Long-read-sinCellTe
-TP single cell Long-read
+
+# sinCellTe 2024: scRNA-seq analysis with long reads
+
+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.