The package encompasses a range of functions for identifying the closest gene, exon, miRNA, or custom features—such as highly conserved elements and user-supplied transcription factor binding sites. Additionally, users can retrieve sequences around the peaks and obtain enriched Gene Ontology (GO) or Pathway terms. In version 2.0.5 and beyond, new functionalities have been introduced. These include features for identifying peaks associated with bi-directional promoters along with summary statistics (peaksNearBDP), summarizing motif occurrences in peaks (summarizePatternInPeaks), and associating additional identifiers with annotated peaks or enrichedGO (addGeneIDs). The package integrates with various other packages such as biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest, and stat to enhance its analytical capabilities.
Package details |
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Author | Lihua Julie Zhu, Jianhong Ou, Jun Yu, Kai Hu, Haibo Liu, Junhui Li, Hervé Pagès, Claude Gazin, Nathan Lawson, Ryan Thompson, Simon Lin, David Lapointe, Michael Green |
Bioconductor views | Annotation ChIPSeq ChIPchip |
Maintainer | Jianhong Ou <jianhong.ou@duke.edu>, Lihua Julie Zhu <julie.zhu@umassmed.edu>, Kai Hu <kai.hu@umassmed.edu>, Junhui Li <junhui.li@umassmed.edu> |
License | GPL (>= 2) |
Version | 3.39.3 |
Package repository | View on GitHub |
Installation |
Install the latest version of this package by entering the following in R:
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