ChIP-seq combines chromatin immuno-precipitation (ChIP) with next-generation sequencing technology to analyze protein interactions with DNA. It has been widely adopted by biologists to identify transcription factor binding location and to map specific histone modification or nucleosome position on the genome. A typical workflow of ChIP-seq includes experimental design, sequencing, and downstream bioinformatics analysis. This workshop focuses on the bioinformatics part by comparing popularly practiced tools, their advantages and limitations. Specifically, we will demonstrate how to perform downstream analysis (after peak calling) with package ChIPpeakAnno and trackViewer.
A mini-lecture will be given at the beginning that will cover basic ideas behind ChIP-seq, comparision of commonly used tools for ChIP-seq data analysis. Then, a hands-on demo will be performed to demonstrate the downstream analysis with ChIPpeakAnno and trackViewer packages. Last will be a Q/A section.
docker pull hukai916/integratedchipseqanalysis_workshop
docker run -e PASSWORD=yourpassword -p 8787:8787 hukai916/integratedchipseqanalysis_workshop
yourpassword. For Windows users, you also need to provide your IP address, you can find it using
docker-machine ip default.
browseVignettes(package = "hukai916/integratedchipseqanalysis_workshop")
The requested page was not founderror, try add ‘help/’ in front of the hostname in the URL (this is a known bug): http://localhost:8787/help/library/integratedchipseqanalysisworkshop/doc/IntegratedChIPseqAnalysisWorkshop.html