Package: ChIPpeakAnno 3.47.2

Introduction | Quick demo | Convert peaks to GRanges | Prepare annotations | Annotate peaks | Add gene symbols | Convert peaks to GRanges | Handle replicates | Obtain final peak set from replicates | Assess the concordance of peak replicates | Find overlapping peaks | Visualize the overlaps using Venn diagram | Use other tools to plot Venn diagram | Visualize the distribution of relative positions for overlapping peaks | Prepare annotation file | Commonly used annotations | Bioconductor supported TxDb and EnsDb | Obtain EnsDb and TxDb from AnnotationHub | Build custom EnsDb and TxDb | Use biomaRt | Convert annotations into GRanges | Use toGRanges function | Use accessor functions | Use getAnnotation function | Visualize peak distributions | Plot peak distributions relative to genomic features | Plot peak distributions over different feature levels | Pie graph with one peak set | Bar graph with a list of peak sets | Plot peak overlaps for multiple features | Annotate peaks | Peak-centric method | Feature-centric method | Relative peak-to-feature location | More customization with bindingRegion | Example 1: find the nearest features | Example 2: find the nearest and overlapping features | Visualize peak-to-feature distances | Use custom annotation data | Add other feature IDs | Example1: find gene symbols for a vector of entrez IDs | Example2: add gene symbols to annotated peaks | Enrichment analysis | Motif analysis | Obtain sequences surrounding the peaks | Discover consensus sequences (motifs) in the peaks | Scan pre-defined sequence patterns in the peaks | Alternative tools | Peak profile comparison | Use hypergeometric test to determine overlap among peak sets | Use permutation test to determine overlap among peak sets | Use custom peak pool | Visualize TSS enrichment signal of multiple experiments | Heatmap | Density plot | Common workflow 1: single TF with replicates | Step1: import data | Step2: prepare annotation file | Step3: visualize peak distribution | Peak distribution relative to features | Peak distribution over multiple feature levels | Peak overlappings for multiple features | Step4: annotate peaks | Find peaks located in bi-directional promoters | Find peaks located in enhancers | Step5: perform enrichment analysis | Step6: conduct motif analysis | Common workflow 2: comparing binding profiles for multiple TFs | Step2: determine if there is significant overlap among peak sets | Step3: visualize and compare the binding patterns | Have questions? | Selected Q & A | How to import peaks? | How to properly annotate peaks from ChIP-seq data? | Should I use annotatePeakInBatch or annoPeaks? | How to prepare annotation data for annotatePeakInBatch? | Can I output either the nearest or overlapping features? | Why is the sum of peak numbers in the Venn diagram NOT equal to the sum of the peaks in the original peak lists? | How does findOverlapsOfPeaks count the number of overlapping peaks? | Is there a way to show the number of peaks in original peak lists? | How to extract the original peak IDs of the overlapping peaks? | How to select the proper number for totalTest when using makeVennDiagram? | How to cite ChIPpeakAnno | Session info