Single cell RNA-seq analysis

This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data via a series of lectures and computer practicals. The total course duration is 5 days, with 4 course days followed by a Bring Your Own Data day where you can apply the skills learned on a dataset of your chosing.

When: 12-16 February 2024 (9.00-17.00)

Location: TrippelrummetLinks to an external site., Entrance C11, BMC, Husargatan 3, Uppsala 75237, Sweden

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
Celltype prediction
Trajectory inference analysis
Comparison of different Seurat, Bioconductor and Scanpy toolkits

REGISTRATION

Open: 2023-11-06

Close: 2024-01-17

Application form: application

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 all Swedish universities. 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 can accommodate maximum of 25 participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.