Upcoming Courses

Single-Cell Data Analysis Lecture & Roundtable

for Charité MD / MD/PhD / PhD students and postdocs

Next occurence: 28.04.2025, 05.05.2025, 19.05.2025, 26.05.2025, 02.06.2025, Monday from 15:00-17:00 (this is the correct time, the Charité Intranet time is incorrect) on MS Teams

Description:
The seminar is intended for pre- and postdoctoral researchers analysing single-cell omics data (scRNA-Seq, scVDJ-Seq, CITE-Seq etc.) as part of their research projects who are facing challenges or uncertainties during the process. It specifically welcomes those without a formal background in bioinformatics who are analysing single cell data with the help of online tutorials, possibly for the first time, and want to touch base on their analysis choices. The course consists of 5 units which are divded into (i) a lecture part providing background on specific parts of single-cell data analysis and (ii) a roundtable part during which participants present their projects with a focus on current challenges and questions. Participants will receive input from the instructor as well as suggestions from their peers. The lecture part covers the following topics: 1) Introduction to single cell transcriptomics data 2) Quality control 3) Dimensionality reduction, clsutering & visualization of high-dimensional data 4) Batch correction methods for dataset combination (integration) 5) Cell type annotation and differential abundance and gene expression analysis.

Requirements:
Participants need to have a single cell omics data set that has been processed to the count matrix stage (i.e. cell by gene matrix, not raw data such as FASTQ files) at the beginning of the seminar and need to be actively working on the analysis of that data.

Registration:
If you want to register for the workshop, please send the following information to lisa.buchauer@charite.de by April 21st:

1. 2-4 sentence description of your research project
2. Description of your single cell dataset (which omics type, which experimental platform (e.g. 10x genomics), how many cells, other relevant information)
3. Description of the analysis framework you are using (e.g. Seurat, scanpy) and outline of the main steps included in your pipeline
4. Current challenges or motivation for joining the workshop

Admitted students will receive the MS Teams link. Please see also the listing in the list of doctoral courses for information on awarded ECTS (Charité doctoral students only).

Ongoing Courses

Journal Club: Data Analysis and Computational Methods in Immunology
for Charité M.Sc. / MD / MD/PhD / PhD students, postdocs and interested staff
ongoing throughout the year, biweekly on Thursdays at 2pm, Südring 2 (CVK) and on MS Teams
Participants present current publications covering computational methods and data analysis approaches in immunology and infectious diseases (e.g. omics data, flow cytometry data, clinical data). Papers with biomedical rather than computational focus can also be presented if they contain interesting data analysis concepts. Each participant presents a paper of their choice in a presentation of ~45 minutes which should also include relevant background and participants’ own evaluation of the work.
Requirements: None, anyone interested in the topic is welcome to join
Registration: Please send an email to lisa.buchauer@charite.de and you will receive exact dates as well as an MS Teams link. Please see also the listing in the list of doctoral courses for information on awarded ECTS (Charité doctoral students only).