Single Cell

Learn all about Single Cell on Galaxy. Start with the tutorial at your own pace. If you need support contact us via the Slack Channel gta_single-cell.

Organiser(s) orcid logoPavankumar Videm avatar Pavankumar Videm
Instructor(s) orcid logoAmirhossein Naghsh Nilchi avatar Amirhossein Naghsh Nilchiorcid logoDiana Chiang Jurado avatar Diana Chiang Juradoorcid logoJennifer Hillman-Jackson avatar Jennifer Hillman-Jacksonorcid logoMarisa Loach avatar Marisa Loachorcid logoPavankumar Videm avatar Pavankumar Videm

Need help with these tutorials?

Open Slack support channel for this track:   #gta_single-cell

Introduction

Introduction lecture to single-cell data analysis and data formats.

Lesson Slides Hands-on Recordings
An introduction to scRNA-seq data analysis
Single-cell Formats and Resources

Raw sequencing data to count matrix

Generate a cell-by-gene matrix from droplet-based single-cell RNA sequencing data.

Lesson Slides Hands-on Recordings
Pre-processing of 10X Single-Cell RNA Datasets
10x
Generating a single cell matrix using Alevin
paper-replication MIGHTS

Your first analysis based on Scanpy toolkit

This section includes standard single-cell data analysis, including preprocessing, clustering and the identification of cell types via known marker genes; and pseudobulk analysis to help in understanding cell-type-specific gene expression changes. The whole analysis uses Anndata objects, Scanpy toolkit and decoupler.

Lesson Slides Hands-on Recordings
Clustering 3K PBMCs with Scanpy
10x
Pseudobulk Analysis with Decoupler and EdgeR
transcriptomics pseudobulk

Your first analysis based on Seurat tools

This section includes single-cell data analysis including preprocessing, clustering and the identification of cell types via known marker genes. The whole analysis uses Seurat objects and Seurat R package.

Lesson Slides Hands-on Recordings
Clustering 3K PBMCs with Seurat
10x