Introduction to bioinformatics workshop
In this workshop, students will learn the fundamental steps of single-cell RNA sequencing (scRNA-seq) data analysis using the Seurat R package. Topics will include quality control and filtering, normalization, dimensionality reduction, clustering, cell type annotation, and basic data visualization. The hands-on session will utilize the HBCA-85 dataset, a publicly available single-cell transcriptomic profile derived from human breast tissue, generated as part of the Human Breast Cell Atlas (HBCA) initiative. This dataset offers a valuable opportunity to explore the cellular diversity of the human breast epithelium and gain experience with real-world single-cell data.
🔗 Dataset download: https://www.dropbox.com/scl/fo/92mtyq9phaf13kigz5wcg/AF3dseRvlbcpLGsS7CMGRDQ?rlkey=6k59eiy8hw1ydmhwyfm58z69o&dl=0
📖 Reference: Kumar, T., Nee, K., Wei, R. et al. A spatially resolved single-cell genomic atlas of the adult human breast. Nature 620, 181–191 (2023). https://doi.org/10.1038/s41586-023-06252-9
You can view a html rendered version of the Rmd file here.