This repository contains lecture slides and practical notebooks for the Shalek Lab workshops on single-cell analysis, held at the Child Health Research Foundation (CHRF) in Dhaka, Bangladesh, from March 29 to April 1, 2026.
Single-cell sequencing technologies enable the measurement of genomic, transcriptomic, and proteomic features at single-cell resolution. These approaches are increasingly used across medicine, public health, agriculture, and the life sciences to study cellular heterogeneity in both health and disease. This workshop series provides an introduction to key concepts and practical analytical workflows for single-cell RNA-seq and immune receptor profiling.
Below are the lecture slides and Google Colab notebooks for the workshop modules.
Introduction to preprocessing workflows for scRNA-seq data, from raw sequencing reads to count matrices. Topics include common library preparation strategies and an overview of Cell Ranger outputs.
Overview of early-stage scRNA-seq analysis, including data import, filtering, visualization, quality assessment, and normalization.
Introduction to clustering, cell annotation, differential expression, and functional interpretation for characterizing cell states and populations.
Concepts and methods for integrating single-cell datasets across samples while correcting for unwanted technical variation, with examples using Seurat and Harmony.
Introduction to single-cell TCR/BCR profiling and its applications in studying immune diversity and adaptive immune responses.
- Mirzapur field visit
- Project work day
This work is licensed under a Creative Commons Attribution 4.0 International License.
