ChIP-seq Review

ChIP-seq with Bioconductor in R

Peter Humburg

Statistician, Macquarie University

Review: Importing data

Load peak calls

peaks <- import.bed(peak_file, genome="hg19")

Create a BamViews object

bam_views <- BamViews(bam_file, bamRanges=peaks)

Load the reads

reads <- readGAlignments(bam_views)
ChIP-seq with Bioconductor in R

Review: Visualising ChIP-seq data

ChIP-seq with Bioconductor in R

ChIP-seq with Bioconductor in R

Review: Differential Binding

ChIP-seq with Bioconductor in R

Review: Enrichment analysis

ChIP-seq with Bioconductor in R

Moving Ahead

ChIP-seq with Bioconductor in R

Well done!

ChIP-seq with Bioconductor in R

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