## Chipster manual

Chipster is a versatile data analysis platform with interactive visualizations and workflows. It offers a comprehensive collection of analysis tools for next generation sequencing (NGS), microarray and proteomics data. The NGS functionality covers analysis from quality control and alignment to downstream applications such as pathway analysis and motif detection (please see the analysis tool summary for details), and more analysis tools are added all the time. The built-in Chipster genome browser allows users visualize reads and results in their genomic context. The microarray functionality covers expression, aCGH, miRNA, methylation and SNP arrays, and allows users to integrate expression data with miRNA and aCGH data.

General

- Getting started with Chipster: Introductory video
- Course materials: Lecture slides and tutorials on selected topics. CSC training material page.
- Analysis sessions: How to continue your analysis later and share it. Manual, video.
- Phenodata editor: Describing your experimental setup. Manual, video.
- Workflows: How to automate and share your analysis pipelines. Manual, video.
- Interactive visualizations. Video.
- Technical manual for admins and developers: How to install your own Chipster server and integrate new tools
- Copyright

NGS data analysis

- Tutorials

- CNA-seq tutorial (pdf)
- RNA-seq tutorials (videos)

- Data import
- Genome browser: Viewing NGS reads and results in genomic context
- Analysis tools for NGS data

- Filtering
- Quality control
- Utilities
- Matching genomic regions
- Alignment
- Variants
- RNA-seq

- How to deal with stranded (directional) RNA-seq data?

- miRNA-seq
- ChIP-, DNase-, and Methyl-seq
- CNA-seq
- 16S rRNA sequencing
- Single cell sequencing

Microarray data analysis

- Supported microarray types
- Example analysis sessions
- Data import
- Tutorials
- Getting started with Chipster: 5 minute tour
- Analysis tools for microarray data

- Normalization
- Quality control
- Preprocessing
- Statistics
- Clustering
- Annotation
- Pathways
- Promoter analysis
- Visualization
- Utilities
- aCGH