covplotfunction to support viewing coverage of a list of
library(ChIPseeker) files <- getSampleFiles() peak=GenomicRanges::GRangesList(CBX6=readPeakFile(files[]), CBX7=readPeakFile(files[])) p <- covplot(peak) print(p)
We provide functions to compare profiles of peaks binding to TSS regions, annotation, and enriched functional profiles. More importantly, ChIPseeker incorporates statistical testing of co-occurrence of different ChIP-seq datasets and can be used to identify co-factors.
I think it would be interesting to incorporate seq2gene with clusterProfiler. But it fail to run due to it call absolute path of python installed in the author’s computer.
Although I found that the chromStart positions in HOMER output have a +1 shift compare to other software, I did not realize this issue since all other software are consistent.
ChIPseeker had been cited by http://www.biomedcentral.com/1471-2164/16/292 and http://www.jbc.org/content/early/2015/06/18/jbc.M115.668558.short, and was used (not cited) in http://nar.oxfordjournals.org/content/early/2015/06/27/nar.gkv642.abstract and http://emboj.embopress.org/content/early/2014/12/18/embj.201490061.abstract.