This workshop will introduce the best practice bioinformatics methods for analysing single cell RNA-seq data via a series of lectures and computer practicals. The total course duration is 5 days which includes 4 days of lectures and exercises followed by a "Bring Your Own Data" day where you get to practice your skills on a dataset of your choosing.

12 February 2024 - 16 February 2024

Trippelrummet, Entrance C11, BMC, Husargatan 3, Uppsala 75237, Sweden

3000 SEK

SYLLABUS

Overview of the current scRNAseq technologies
Basic overview of pipelines for processing raw reads into expression values
Quality control and normalization
Dimensionality reduction techniques
Data integration and batch correction
Differential gene expression
Clustering techniques
Cell type prediction
Trajectory inference analysis
Comparison of Seurat, Bioconductor and Scanpy toolkits

REGISTRATION

Course fee: This workshop has a fee of 3000 SEK and will be invoiced to the selected participants (Please note that NBIS cannot invoice individuals). Applications without complete invoice information will not be considered. Course fees cover all coffee breaks, all lunches and 1 course dinner.

This is a national course. The course is open for PhD students, postdocs, group leaders and core facility staff within Swedish academia. Even if we do accept application from other countries, we give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries.

Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

Practical exercises will be performed using either R or Python, so we only accept students that fulfill the entry requirements below.

Entry requirements:

You are familiar with basic UNIX command line (bash)
You are familiar with either R and/or Python
You already understand the basics of NGS technologies
You are familiar with analyses of bulk RNA-sequencing data
You have full access to your computer (admin permissions). Instructions on installation will be sent by email to accepted participants.

Due to limited space, the course accommodates a maximum of 25 participants. If we receive more applications, participants will be selected based on selection criteria such as correct entry requirements, motivation to attend the course as well as gender and geographical balance.

Application open: 2023-11-13

Application close: 2024-01-17

Application form: https://nbis.typeform.com/to/VYqpkdkh

CONTACT

Åsa Björklund, Susanne Reinsbach, Roy Francis

edu.sc [at] nbis.se

CODE OF CONDUCT

By participating in this workshop, you will be agreeing to the NBIS Code of Conduct.

2024 | National Bioinformatics Infrastructure Sweden