iaradsouza1 / intro-single-cell

Introduction to single-cell RNA-seq analysis

Single-cell RNA-seq introduction course

This course covers the basics of single-cell RNA-seq analysis. This material was meant to be continuously improved by the students from the Dalmolin Systems Biology Group.

This book is based on the following references:

• The experimental design of single-cell studies: Tutorial: guidelines for the experimental design of single-cell RNA sequencing studies
• Orchestrating Single-Cell Analysis with Bioconductor - Basics;
• Single-cell best practices
• Seurat cheatsheet
• Introduction to single-cell from Wellcome Connecting Science
• SingleR
• This awesome playlist on YouTube (in python): link

Install R packages using conda or mamba

Note the environment.yml file. It has a list of R packages that are going to be used in this course. Install them by:

conda env create -f environment.yml

Activate the intro-single-cell environment:

conda activate intro-single-cell

Download the data

In your machine, download this folder and extract it to the same location of the course folder.

Datasets to practice

List of datasets to practice: link

intro-single-cell's Issues

Create a quarto document to contain nice suggestions of tools to be used in each part of the analysis

Description

Lots of tools were not presented for the main analysis notebooks. Create a separate notebook to hold these suggestions.

Filter only the positive differences (those whose the cluster of interest has a greater percentage of cells expressing the marker)

On Bioc markers, add filtering step to retrieve only the positive differences.

Add notebook detailing the steps to install packages

Improve the introductory text from the notebook 2