Chapter 10 Functional enrichment analysis of genomic coordinations

Functional analysis using NGS data (eg, RNA-Seq and ChIP-Seq) can be performed by linking coding and non-coding regions to coding genes via ChIPseeker(Yu, Wang, and He 2015) package, which can annotates genomic regions to their nearest genes, host genes, and flanking genes respectivly. In addtion, it provides a function, seq2gene, that simultaneously considering host genes, promoter region and flanking gene from intergenic region that may under control via cis-regulation. This function maps genomic regions to genes in a many-to-many manner and facilitate functional analysis. For more details, please refer to ChIPseeker(Yu, Wang, and He 2015).

References

Yu, Guangchuang, Li-Gen Wang, and Qing-Yu He. 2015. “ChIPseeker: An R/Bioconductor Package for Chip Peak Annotation, Comparison and Visualization.” Bioinformatics 31 (14): 2382–3. https://doi.org/10.1093/bioinformatics/btv145.