Chipseeker

[Bioc 3.5] NEWS of my BioC packages

I have 8 packages published within the Bioconductor project.

A new package treeio was included in BioC 3.5 release.

[Bioc 34] NEWS of my BioC packages

I have 7 packages published within the Bioconductor project.

A new package meshes was included in BioC 3.4 release.

[Bioc 33] NEWS of my BioC packages

Today is my birthday and it happened to be the release day of Bioconductor 3.3. It’s again the time to reflect what I’ve done in the past year.

covplot supports GRangesList

To answer the issue, I extend the covplot function to support viewing coverage of a list of GRanges objects or bed files.

library(ChIPseeker)
files <- getSampleFiles()
peak=GenomicRanges::GRangesList(CBX6=readPeakFile(files[[4]]),
                                CBX7=readPeakFile(files[[5]]))

p <- covplot(peak)
print(p)

[Bioc 32] NEWS of my BioC packages

In BioC 3.2 release, all my packages including GOSemSim, clusterProfiler, DOSE, ReactomePA, and ChIPseeker switch from Sweave to R Markdown for package vignettes.

GOSemSim

To make it consistent between GOSemSim and clusterProfiler, ‘worm’ was deprecated and instead we should use ‘celegans’. As usual, information content data was updated.

ChIPseq data mining with ChIPseeker

ChIP-seq is rapidly becoming a common technique and there are a large number of dataset available in the public domain. Results from individual experiments provide a limited understanding of chromatin interactions, as there is many factors cooperate to regulate transcription. Unlike other tools that designed for single dataset, ChIPseeker is designed for comparing profiles of ChIP-seq datasets at different levels.

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.

functional enrichment analysis with NGS data

I found a Bioconductor package, seq2pathway, that can apply functional analysis to NGS data. It consists of two components, seq2gene and gene2pathway. seq2gene converts genomic coordination to genes while gene2pathway performs functional analysis at gene level.

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.

parsing BED coordinates

In supplemental file of ChIPseeker paper, I compare distances to TSS reported by several ChIP annotation software, including ChIPseeker, ChIPpeakAnno, HOMER and PeakAnalyzer.

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.

upsetplot in ChIPseeker

ChIPseeker is an R package for ChIP peak annotation, comparison and visualization.

We have implemented several visualization methods, including vennpie that was designed for viewing annotation overlap as shown below:

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

My R/Bioconductor package, ChIPseeker, published in Bioinformatics.

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.