Chipster manual

Chipster is an easy-to-use analysis software for high-throughput data. There are currently two interfaces: a Web App and a Java client. The latter requires Java Web Start, and it will be phased out by 15 Nov 2020. Both interfaces offer the same comprehensive collection of analysis tools for

• RNA-seq
• Single cell RNA-seq
• Small RNA-seq (miRNA and VirusDetect)
• Community analysis of 16S data
• ChIP-seq and DNase-seq
• Exome and whole genome seq (variants and copy number aberrations)
• Microarrays

• Introductory videos for getting started with Chipster: Web App, Java client
• Course materials: Lecture slides, videos and exercises on selected topics.
• Technical manual for admins and developers: How to install your own Chipster server and integrate new tools
• Copyright
• Java client instructions:
  • 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.
  • Data import
  • Genome browser: Viewing NGS reads and results in genomic context

• Tutorials
  • RNA-seq data analysis for differential expression
  • Dealing with stranded (directional) RNA-seq data
  • RNA-seq data analysis step by steps (videos)
  • Community analysis of 16S data step by steps (videos)
  • CNA-seq tutorial (pdf)
• Analysis tools for NGS data
  • Quality control
  • Filtering
  • Utilities
  • Matching sets of genomic regions
  • Alignment
  • Variants
  • RNA-seq
  • Small RNA-seq
  • Single cell RNA-seq
  • ChIP- and DNase-seq
  • CNA-seq
  • 16S rRNA sequencing

• Supported microarray types
• Example analysis sessions
• Data import (Java client)
• Tutorials (Java client)
• Getting started with Chipster: 5 minute tour (Java client)
• Analysis tools for microarray data
• Normalization
• Quality control
• Preprocessing
• Statistics
• Clustering
• Annotation
• Pathways
• Promoter analysis
• Visualization
• Utilities
• aCGH