DiffBind: Differential Binding Analysis Of ChIP Seq Peak Data Diff Bind Manual

• 1 Introduction
• 2 Processing overview
• 3 Example: Obtaining differentially bound sites
  • 3.1 Reading in the peaksets
  • 3.2 Counting reads
  • 3.3 Establishing a contrast
  • 3.4 Performing the differential analysis
  • 3.5 Retrieving the differentially bound sites
• 4 Example: Plotting
  • 4.1 Venn diagrams
  • 4.2 PCA plots
  • 4.3 MA plots
  • 4.4 Volcano plots
  • 4.5 Boxplots
  • 4.6 Heatmaps
• 5 Example: Differential binding analysis using a blocking factor
• 6 Example: Occupancy analysis and overlaps
  • 6.1 Overlap rates
  • 6.2 Deriving consensus peaksets
  • 6.3 A complete occupancy analysis: identifying sites unique to a sample group
  • 6.4 Comparison of occupancy and affinity based analyses
• 7 Technical notes
  • 7.1 Loading peaksets
  • 7.2 Merging peaks
  • 7.3 DESeq2 analysis
  • 7.4 edgeR analysis
  • 7.5 DESeq analysis
• 8 Vignette Data
• 9 Using DiffBind and ChIPQC together
• 10 Acknowledgements
• 11 Session Info