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Mon 2 Dec, Fri 6 Dec, Mon 9 Dec 2024
09:30 - 17:30

Venue: Bioinformatics Training Facility - Online LIVE Training

Provided by: Bioinformatics


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2025


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Single-cell RNA-seq analysis (ONLINE LIVE TRAINING)
Prerequisites

Mon 2 Dec, Fri 6 Dec, Mon 9 Dec 2024

Description

Recent technological advances have made it possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing. This course offers an introduction to single-cell RNA sequencing (scRNA-seq) analysis. Participants will gain hands-on experience with key software packages and methodologies for processing, analyzing, and interpreting scRNA-seq data. Key topics include data preprocessing, quality control, normalization, dimensionality reduction, batch correction and data integration, cell clustering and differential expression and abundance analysis. By the end of the course, students will be equipped with the skills to independently conduct and critically analyse data from scRNA-seq experiments.


If you do not have a University of Cambridge Raven account please book or register your interest here.

Additional information
  • Our courses are only free for registered University of Cambridge students. All other participants will be charged according to our charging policy.
  • Attendance will be taken on all courses and a charge is applied for non-attendance. After you have booked a place, if you are unable to attend any of the live sessions, please email the Bioinfo Team.
  • Further details regarding eligibility criteria are available here.
Target audience
Prerequisites

Essential

Desirable

Sessions

Number of sessions: 3

# Date Time Venue Trainers
1 Mon 2 Dec   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training Abigail Edwards,  Chandra Chilamakuri,  Yunxiao (Betty) Wang,  Dr A.J. Reid,  Katarzyna Kania
2 Fri 6 Dec   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training Abigail Edwards,  Chandra Chilamakuri,  Dr A.J. Reid,  R. Ragheb
3 Mon 9 Dec   09:30 - 17:30 09:30 - 17:30 Bioinformatics Training Facility - Online LIVE Training Abigail Edwards,  Chandra Chilamakuri,  Dr A.J. Reid,  R. Ragheb
Topics covered

Bioinformatics, Data handling, Data mining, Data visualisation, Functional genomics, Transcriptomics

Objectives

During this course you will learn about:

  • Different scRNA-seq technologies and what kind of data you obtain from each.
  • Processing raw sequencing data from the commonly-used 10x Chromium platform using cellranger.
  • Use several R/Bioconductor packages for downstream analysis of scRNA-seq data, including: data normalization, correction for batch effects, dimensionality reduction methods (PCA, t-SNE and UMAP), cell clustering and differential expression and abundance analysis.
Aims

After this course you should be able to:

  • Describe the range of single-cell sequencing technologies available, their pros and cons and which you may want to use for your experiments.
  • Process raw single-cell sequencing data and assess the quality of your data.
  • Normalise scRNA-seq data.
  • Visualise the data and apply dimensionality reduction.
  • Apply methods for batch correction and data integration.
  • Identify groups of similar cells by clustering and identify marker genes to differentiate them.
  • Apply differential expression and cell abundance between conditions.
Format

Presentations, demonstrations and practicals

System requirements

Participants must have their own computers to work on and a stable internet connection for the duration of the course.

Timetable

Day 1 Topics
Session 1 Introduction to single-cell technologies
Session 2 Library structure and cell calling using the cellranger software.
Session 3 Quality control and exploratory analysis of scRNA-seq using R/Bioconductor
Day 2 Topics
Session 1 Data normalisation
Session 2 Feature selection and dimensionality reduction
Session 3 Batch correction and data integration
Day 3 Topics
Session 1 Cell clustering
Session 2 Identification of cluster marker genes
Session 3 Differential expression and abundance analysis
Registration Fees
  • Free for registered University of Cambridge students
  • £ 60/day for all University of Cambridge staff, including postdocs, temporary visitors (students and researchers) and participants from Affiliated Institutions. Please note that these charges are recovered by us at the Institutional level
  • It remains the participant's responsibility to acquire prior approval from the relevant group leader, line manager or budget holder to attend the course. It is requested that people booking only do so with the agreement of the relevant party as costs will be charged back to your Lab Head or Group Supervisor.
  • £ 60/day for all other academic participants from external Institutions and charitable organizations. These charges must be paid at registration
  • £ 120/day for all Industry participants. These charges must be paid at registration
  • Further details regarding the charging policy are available here
Duration

3

Frequency

A number of times per year

Related courses
Theme
Bioinformatics

Booking / availability