## 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 ChIP-seq, RNA-seq, miRNA-seq and methyl-seq 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.

- Getting started with Chipster: 5 minute tour, tutorials
- Software requirements
- Supported microarray types
- Data import
- Analysis tools for microarray data

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

- Analysis tools for NGS data

- Filtering
- Quality control
- Utilities
- Matching genomic regions
- Alignment
- RNA-seq
- miRNA-seq
- ChIP-seq
- Methyl-seq

- Phenodata editor: Describing your experimental setup
- Workflows: Automating your analysis pipelines and sharing them
- Analysis sessions: Continuing your work later/elsewhere and sharing it
- Genome browser: Viewing NGS reads and results in genomic context
- For developers
- Copyright