Single-Cell RNA-Seq Data Analysis: A Practical Introduction
From 10x/Cell Ranger processing to Seurat-based clustering and multi-sample integration

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Single-cell RNA sequencing data analysis workshop in Berlin

Learn a complete, beginner-friendly single-cell workflow, from raw data processing and QC to cluster annotation, differential expression, and integration across samples.

In a nutshell

  • Understand sequencing technologies for single-cell analysis (plate-based vs droplet-based)

  • Process, QC and analyze scRNA-seq data with a structured, reproducible workflow

  • Identify, visualize and annotate cell clusters using practical marker-based strategies

  • Integrate multi-sample data and handle batch effects with confidence

When?
March 15-17, 2027

9:00 am-5:00 pm

Where?
Berlin, Germany

Register Now

Scope and Topics

Participants working through a hands-on bioinformatics exercise

This workshop provides a thorough, hands-on introduction to single-cell RNA sequencing (scRNA-seq) data analysis. You will learn how to process, analyze, and integrate single-cell datasets using widely adopted tools and best practices.

We cover sequencing technologies, quality control and preprocessing, dimensionality reduction, clustering, trajectory inference, differential expression analysis, and multi-sample integration.

By the end of the workshop, you will be able to:

  • Process 10x Chromium data with Cell Ranger and interpret key QC metrics

  • Perform single-sample analysis in Seurat (filtering, normalization, PCA/UMAP, clustering, markers)

  • Create diagnostic plots and make informed analysis decisions (not "click-and-hope")

  • Integrate datasets across samples/conditions, handle batch effects, and compare clusters via differential expression

Go to registration.

Our Philosophy

Get trained by experts

Our trainers bring proven academic and/or industry experience in NGS and single-cell data analysis, so your questions are answered with practical, up-to-date context.

Open source NGS tools

We focus on open-source tools that are free to use in academia and industry, so you can continue applying the workflow after the course.

Learn effectively with well-curated materials

We provide carefully prepared datasets and step-by-step exercises to help you learn efficiently and build confidence quickly.

Hands-on bioinformatics training environment

Workshop Design

Participants during a practical bioinformatics workshop

This workshop is tailored to beginners in biological data analysis and consists of three course modules:

  1. Single-cell RNA-seq foundations:
    Get the foundations right: single-cell technologies, file formats, basic Linux navigation, and a guided introduction to Cell Ranger for 10x Chromium processing and QC.
  2. Single-sample analysis with Seurat in R:
    Learn the standard Seurat workflow for one dataset: preprocessing, dimensionality reduction, clustering, marker detection, and diagnostic plots.
  3. Data integration and multi-sample analysis:
    Integrate multiple samples, address batch effects, compare clusters/conditions via differential expression, and get an introduction to multi-modal analysis, supported by hands-on exercises.

Detailed Course Program


Single-cell RNA-seq foundations

  • Sequencing technologies from a single-cell perspective
  • Plate-based vs droplet-based methodologies: what changes for analysis
  • Linux command line basics and navigating the file system
  • Core bioinformatics file formats (FASTQ, FASTA, GTF)
  • From reads to a count matrix: alignment, filtering, expression quantification
  • Processing and QC of 10x Chromium data using Cell Ranger

Single-sample analysis with Seurat in R

  • Getting comfortable with data handling in R
  • Preprocessing: cell filtering, normalization, feature selection
  • Dimensionality reduction: PCA and choosing meaningful dimensions
  • Non-linear embedding with t-SNE and UMAP
  • kNN-based clustering in Seurat
  • Marker detection and practical strategies for cluster annotation
  • Diagnostic plots you can trust: what to plot, how to interpret it
  • Trajectory inference and an introduction to RNA velocity

Data integration and multi-sample analysis

  • Integration concepts: combining datasets from different sources
  • Cell label transfer
  • Batch effects: how to recognize them and how "soft integration" works
  • Differential expression between clusters and conditions
  • Multi-modal analysis: incorporating additional -omics layers
  • Guided challenge exercises to apply your new skills

Trainers

Dr. Adam Nunn

Dr. Adam Nunn (ecSeq Bioinformatics GmbH)
Adam is a bioinformatician specialized in DNA-Seq, bulk RNA-Seq, and single-cell RNA-Seq, with a strong focus on robust, pipeline-based analysis. Publications

Rosaria Tornisiello

Rosaria Tornisiello (Max Planck Institute for Molecular Genetics)
Rosaria is a PhD researcher working with genomic and single-cell data to study epigenetic regulation during mammalian development. Publications

Requirements

This workshop is aimed at biologists and data analysts with no or little experience in developing computational pipelines for data analysis.

A basic understanding of molecular biology (DNA, RNA, gene expression, PCR, ...) is assumed, as examples are discussed in that context.

Some familiarity with a command line interface (Linux/macOS) is helpful, and a minimal understanding of programming concepts can be beneficial, but neither is required. We start from the essentials and guide you step-by-step.

Clarity note:

You will work in R/Seurat, but this is not a programming course - the focus is on analysis workflows and interpretation.

Included in the course

  •   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

Computer workstation provided for the practical exercises

Attendance

Location: PC-College, Stresemannstrasse 78, 10963 Berlin, Germany

Language: English

Available Seats: 30 (first-come, first-served)

Registration Fee: 1089 EUR (excluding VAT)

Travel expenses and accommodation are not covered.

Travel Information - Berlin

Key dates

Registration: Open now

Closing Date of Registration: March 12, 2027, or when all seats are filled

Workshop: March 15-17, 2027, from 9:00 am to 5:00 pm

What participants in our Single-Cell RNA-Seq courses are saying

"The workshop completely fulfiled my expectations. It had the right scope for me and my background knowledge was sufficient. I could get a solid overview of the basics of the lab techniques of scRNA-seq and at the same time have a lot of hands on experience regarding analysis of real data. The program covered all the steps from raw data processing to biological interpretation of the results. The organization was very smooth and scheduling for three days adequate." Heike Sprenger, German Federal Institute for Risk Assessment

"The setup of the course was absolutely perfect. The material we get, the walk-through and everything. The teachers are excellent in explaining complicated theory and methods but you truly gain a lot of knowledge that I now use in my work. Additionally, I loved how much you do for the participants doing our stay with lunch, conference dinner and more. Courses from ecSEQ has my highest recommendation!" Amalie Baisgaard, Aalborg University

"The course offered a great balance between theory and hands-on practice, making complex topics like quality control, dimensionality reduction, and differential expression analysis easy to understand. The instructors were incredibly approachable and willing to answer questions, which created a supportive learning environment. The resources provided were thorough, and the networking opportunities were an added bonus. I now feel much more confident in analyzing single-cell RNA-seq data. I highly recommend this workshop to anyone interested in gaining a solid foundation in this cutting-edge area of research." Andrea ACURIO, Institute of Entomology, Biology Centre, CAS

See all course reviews

When you register for this workshop, you agree to our Workshop Terms and Conditions. Please read them before registering.


ecSeq Bioinformatics contact information

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

ecSeq Bioinformatics GmbH

Sternwartenstr. 29

D-04103 Leipzig

Germany

Email: events@ecSeq.com