SIB/EPFL course by Vincent Gardeux
SIB course website: https://www.sib.swiss/training/course/20231108_ASAP
Recording of the lecture:
2023 Nov. 08th & 2023 Nov. 15th - Online
In recent years, single-cell transcriptomics has become a widely used technology to study heterogeneous and dynamic biological systems. A large number of new tools and approaches have been developed for analyzing this new type of data.
The goal of this course is to provide theoretical and practical knowledge in the basic analysis of single-cell RNA-seq datasets. Specifically, using an online platform, ASAP (asap.epfl.ch), to make the entire analysis code-free, reproducible and shareable.
This course covers the standard analysis of a single-cell RNA-seq dataset using ASAP. ASAP (Automated Single-cell Analysis Portal) is a web-based (asap.epfl.ch), collaborative portal aimed at democratizing single-cell omics data analyses and rendering it more accessible to researchers. ASAP does not require any installation and enables standardized analyses that can be run in minutes by any user without requiring significant computing power. The entire single-cell analysis pipeline is available in ASAP, allowing users to choose from a panel of tools, and guiding them through tutorials.
In the hands-on part of this course, we will use a toy dataset consisting of 7,000 cells from the "Fly Cell Atlas" repository. These cells all come from the Body part, which was dissociated as a whole and sequenced using 10x Genomics technology over 10 batches, mixing males and females. This set of 7,000 cells was carefully selected/filtered from the original Body dataset that consists of 96,926 cells. They belong to a certain number of differently annotated cell types. The goal of the hands-on session is to 1) Preprocess the dataset using a standard pipeline, 2) find out how many cell types there are in the data set, and 3) annotate the cell types using ASAP or any other literature/expert curated knowledge about cell-types/marker genes.
2023.11.08 & 2023.11.15 - Online
This course will take place 100% online.
- 2023.11.08 (3h): After a short introduction to single-cell genomics, and more particularly single-cell transcriptomics, we will see what is ASAP and how we can use it to perform single-cell analysis on an example dataset.
- 2023.11.15 (3h): Hands-on session on a single-cell dataset where participants will perform all steps of the single-cell analysis pipeline themselves, and annotate cell types.
At the end of the course, the participants are expected to:
- run a single-cell RNA-seq analysis pipeline using ASAP
- choose the best tools and parameters for each analysis step
- carry out cell-type annotation and downstream analyses
- disseminate their experience to the members of their group
Pre-requisites - background knowledge
- This course is designed for beginners. Basic knowledge of single-cell analysis (equivalent to the SIB courses Single-cell Transcriptomics or NGS - Single-cell RNA-Seq Analysis) is required.
Pre-requisites - material & software
- This course will be streamed, the participants are thus required to have their own computer with an Internet connection. ASAP is a fully online tool, so no other installation is needed.
- Vincent Gardeux, Senior Scientist, EPFL, Lausanne, 🇨🇭 Switzerland
- Monique Zahn, SIB training group, 🇨🇭 Switzerland
Additional information
For more information, please contact vincent.gardeux@epfl.ch.