Single-Cell RNA-Seq Data Analysis: A Practical Introduction
From Data Processing to Multi-Sample Integration

Master the tools and techniques to confidently analyze single-cell RNA-seq data and gain new insights into complex biological systems

In a nutshell

  • Explore sequencing technologies for single-cell analysis
  • Process QC and analyze single-cell RNA-seq data
  • Learn how to identify and annotate cell clusters
  • Discover how to integrate and analyze multi-sample data

November 8-10, 2023
9 am - 5 pm

Berlin, Germany

The Single-Cell RNA-Seq Workshop is designed to provide a thorough introduction to the analysis of single-cell RNA sequencing data. Through a combination of lectures and hands-on exercises, participants will learn how to process, analyze and integrate single-cell data using industry-standard tools and techniques. Topics covered include sequencing technologies, data quality control, preprocessing, dimensional reduction, clustering, trajectory inference, differential expression analysis, and multi-sample integration.

By the end of the workshop, attendees will have the skills and confidence to perform custom analyses and gain new insights into complex biological systems. This workshop is ideal for researchers and students with little or no prior experience in single-cell RNA-seq analysis, as well as those seeking to update their skills and knowledge.

Get trained by experts

Our trainers have a proven record of academic and/or industrial experience in NGS data analysis. Because up-to-date expert knowledge is needed to answer your questions and know what is important in the field.

Open source NGS tools

We only use open source tools that are free to use for academia and industry.

Learn effectively with well-curated materials

For an optimal learning experience we carefully prepare our learning materials and example data.

This workshop has been adapted to the needs of beginners in the field of (biological) data analysis and comprises these three course modules:

  1. Applications of NGS in Single-Cell analysis:
    During the first part of the workshop, participants learn about sequencing technologies, bioinformatics file formats, and sample library processing. They also become familiar with the Cell Ranger platform and how to navigate the Linux command line and file system.
  2. Single-sample analysis with R-Seurat:
    The second part of the workshop focuses on single-sample analysis using R-Seurat. Participants learn standard preprocessing steps, dimensional reduction techniques, clustering, and marker detection, while creating extensive diagnostic graphics with R.
  3. Data integration and multi-sample analysis:
    The final part of the workshop covers data integration and multi-sample analysis, including the integration of different sources of data, handling of batch effects and soft integration, and differential expression analysis between cell clusters and conditions. Participants also learn about multi-modal analysis and apply their new skills to challenging exercises.

Detailed Course Program

Applications of NGS in Single-Cell analysis

  • Introduction to sequencing technologies from a single-cell perspective
  • Understanding plate-based and droplet-based methodologies
  • Introduction to the Linux command line and navigating the file system
  • Overview of bioinformatics file formats (e.g. FASTQ, FASTA, GTF)
  • Processing sample libraries: Alignment, filtering, and expression count matrices
  • Using the Cell Ranger platform to process and QC Chromium 10X data

Single-sample analysis with R-Seurat

  • Familiarise with data processing in R
  • Standard preprocessing steps: filtering cells, data normalisation, feature selection
  • Dimensional reduction: principle component analysis, determining the dimensionality
  • Non-linear dimensional reduction with tSNE and UMAP
  • Clustering in Seurat by k-nearest neighbours
  • Marker detection for cluster annotation
  • Creating extensive diagnostic graphics with R
  • Single-cell trajectory inference and RNA velocity

Data integration and multi-sample analysis

  • Data integration: combining different sources of data
  • Cell-label transfer
  • Handling batch effects and soft integration
  • Differential expression between cell clusters and conditions
  • Multi-modal analysis: incorporating high dimensional -omics data
  • Applying your new skills by working on challenging exercises


Dr. Adam Nunn (ecSeq Bioinformatics GmbH)
is a PhD student at the Marie Skłodowska-Curie Innovative Training Network 'Epidiverse'. He developed several bioinformatics pipelines using Nextflow for this European network.

Dr. Mario Fasold (ecSeq Bioinformatics GmbH)
Mario works in the analysis of microarray data since 2007 and developed several bioinformatics tools such as the Bioconductor package AffyRNADegradation and the Larpack program package. Since 2011 he specialized in the field of NGS data analysis and helped analysing sequencing data of several large consortium projects.


The target audience are biologists or data analysts with no or little experience in developing computational pipelines for data analysis. A superficial understanding of molecular biology (DNA, RNA, gene expression, PCR, ...) is assumed, as examples will be given in the context of this field.

Some familiarity with a command line interface (e.g. Linux, Mac OS X) and a minimal understanding of object-oriented programming (with e.g. Python or Java) is recommended but not required.

  •   Printed course materials
  •   Catering during the workshop
  •   Conference dinner
  •   High-performance computer (no laptop needed)
  •   Downloadable environment for seamless continuation / repetition after the course
  •   Certificate


Location: PC-College, Stresemannstra├če 78, 10963 Berlin, Germany
Language: English
Available Seats: 30 (first-come, first-served)

Registration Fee: 1089 EUR (excluding VAT)

Travel Information - Berlin

Key dates

Opening Date of Registration: May 1, 2023
Closing Date of Registration: November 1, 2023
Workshop: November 8-10, 2023 from 9 am to 5 pm

"The workshop exceeded my expectations. It was well designed and well laid out for 4 days. Apart from theory, there were excercises at each stage which worked well for basic as well as advanced users. The instructors were competent and their excellent communication helped us to absorb this advanced course. They also provided opportunity to discuss our custom problems." Aashish Srivastava, Haukeland University Hospital, Bergen, Norway

"I really enjoyed the nature of the workshop, I felt that everything was very approachable for the attendees to learn even if the experience was lacking. I witnessed some of my classmates who have no experience ask very detailed questions through the course of the workshop, so I think it is a testimonial to how informational the content of the workshop was." Noah Legall, University of Georgia, USA

"Another great course, with very pleasant and helpful trainers, as well as great international participants. In addition to the theoretical introduction to pipeline development, sufficient time is provided for practical exercises. The course materials provided allow a fast transfer of the course content into practice." Manuela Harloff, University Hospital Augsburg, Germany

When you register for this workshop you are agreeing with our Workshop Terms and Conditions. Please read them before you register.

Any Questions? Please feel free to contact our events team.

ecSeq Bioinformatics GmbH
Sternwartenstr. 29
D-04103 Leipzig