Welcome to Chipster
Chipster is a user-friendly analysis software for high-throughput data such as Visium, single-cell and bulk RNA-seq. Chipster provides a web interface to over 500 analysis tools, and the actual analysis jobs run on the server side making use of CSC's computing environment (watch introduction video).
If you would like to use Chipster hosted by CSC, you need a user account. Please note that Chipster is also available for local server installation free of charge.
Training:
- 4.-5.3.2025 Single-cell RNA-seq data analysis
- 1.-2.4.2025 Analysis of bulk RNA-seq data
- 8.-9.4.2025 Microbial community analysis
- 15.5.2025 Spatial transcriptomics (Visium) data analysis
- MOOC Single-cell RNA-seq data analysis using Chipster
- MOOC Spatially resolved transcriptomics data analysis using Chipster
News and resources:
- video tour of Chipster Web app
- ASV-based microbial community analysis using DADA2: Tutorial videos
- Instructions for moving data from Puhti to Chipster
- Video on how to convert tables to Chipster format and create phenodata file
- Lecture videos of advanced single-cell RNA-seq data analysis course
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RNA-seq resources:
- Lecture videos
- Step-by-step instructions for differential expression analysis
- RNA-seq data analysis guidebook with Chipster instructions
- Archive
Maintenance:
- Thursday 6.3.2025 10 - 16 (UTC+2) A server platform maintenance. Chipster can be unavailable intermittently.
- Tuesday 25.2.2025 9 - 10 (UTC+2) Chipster service break.
- Tuesday 18.2.2025 9 - 10 (UTC+2) Chipster service break. Update: cancelled.