ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis

(2014) Guangchuang Yu et al.   BIOINFORMATICS

PAVIS: a tool for Peak Annotation and Visualization

(2013) Weichun Huang et al.   BIOINFORMATICS

Synergistic and tunable human gene activation by combinations of synthetic transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

(2010) Mali Salmon-Divon et al.   BMC BIOINFORMATICS

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS