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.
In ggtree, we provide a function annotation_image for annotating phylogenetic tree with images.
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:
11年的老机器，闲置了两年，终于在我来HKU的时候发挥了作用，我第一次遇到做生物信息学要自己背电脑去干活。于是每天学校宿舍两头背，当时
唯一的问题是headphone亮着红光，这个本身不难解决，用alsamixer把S/PDIF给mute了就OK了，但坑爹的是每次启动都是亮着红光，这让我很是纠结，我只能通过rc.local，让它每次开机都把alsamixer的状态都给恢复一下：
flip function is a feature request from ggtree user. It accepts a tree view and two node numbers and exchange the positions of the selected clades.
require(ggtree)
set.seed(2015-07-01)
tr <- rtree(30)
p <- ggtree(tr) + geom_text(aes(label=node))
gridExtra::grid.arrange(p, flip(p, 38, 33), ncol=2)
Amos是纯于比较难安装那种，因为依赖关系比较复杂。
首先编译需要qt4-dev和boost graph toolkit：
sudo apt-get install libqt4-dev
sudo apt-get install libboost-graph-dev
再者是perl模块：
sudo cpan -i DBI
sudo cpan -i Statistics::Descriptive
This is a feature request from clusterProfiler user. It’s similar to what I implemented in clusterProfiler for comparing biological themes. For comparing different enrichment results, the x-axis represent different gene clusters while for a single enrichment result, the x-axis can be gene count or gene ratio. This is actually similar to traditional barplot, with dot position as bar height and dot color as bar color. But dotplot can represent one more feature nicely by dot size and it can be a good alternative to barplot.
