Publications by R on Guangchuang Yu
modified wp-codebox to highlight R code as in Pretty-R
I found wp-codebox could highlight R code two years ago. This plugin is based on GeSHi to highlight source code internally. Now there are many ways to highlight R syntax in the website. Pretty-R provided by Inside-R is a popular tool in the community. I like the color style of Pretty-R more than which provided by GeSHi. GeSHi also links functions...
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project euler — problem 68
Consider the following “magic” 3-gon ring, filled with the numbers 1 to 6, and each line adding to nine. Working clockwise, and starting from the group of three with the numerically lowest external node (4,3,2 in this example), each solution can be described uniquely. For example, the above solution can be described by the set: 4,3,2; 6,2,1;...
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Run remote R in Emacs with ESS
Emacs is a great front-end for most of the command line tools. Although R-Studio is pretty good, I think Emacs/ESS is better. I’ve always used Emacs/ESS to run R, since 2007 on Ubuntu, on Windows, and on my MacBook Pro. It gives me the same experiences across all platforms. I love the way Emacs formatting source codes, and literate programming...
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Bug of R package ChIPpeakAnno
comments in the authors original blog post. If you are reading this you are highly encouraged to had over there> I used R package ChIPpeakAnno for annotating peaks, and found that it handle the DNA strand in the wrong way. Maybe the developers were from the computer science but not biology background. ?View Code RSPLUS1 2 3 4 5 6 7 8 9 1...
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ChIPseeker for ChIP peak annotation
ChIPpeakAnno WAS the only one R package for ChIP peak annotation. I used it for annotating peak in my recent study. I found it does not consider the strand information of genes. I reported the bug to the authors, but they are reluctant to change. So I decided to develop my own package, ChIPseeker, and it’s now available in Bioconductor. ?View...
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visualization methods in ChIPseeker
After two weeks developed, I have added/updated some plot functions in ChIPseeker (version >=1.0.1). ChIP peaks over Chromosomes ?View Code RSPLUS1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 > files=getSampleFiles() > peak=readPeakFile(files[[1]]) > peak GRanges with 1331 ranges and 2 metadata columns: seqnames ...
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再不相信预编译的R
去年ubuntu下apt-get了R-3.0.2, 用了没多久就发现了system命令有问题，通常情况下调用系统命令是正常的，但是我调用bowtie的时候，就会报错： Warning: Could not open read file "/tmp/8156.inpipe1" for reading; skipping... Error: Encountered internal Bowtie 2 exception (#1) Command: /usr/bin/bowtie2-align --w...
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enrichment map
In PLOB‘s QQ group, someone asked how to change the color of enrichment map in Cytoscape. I am very curious how enrichment map can helps to interpret enrichment results. It took me 2 hours to implement it using R and I am surprised that the enrichment map is better than anticipated. Now in the development version of clusterProfiler, DOSE, and ...
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why clusterProfiler fails
Recently, there are some comments said that sometimes clusterProfiler failed in KEGG enrichment analysis. kaji331 compared cluserProfiler with GeneAnswers and found that clusterProfiler gives larger p values. The result forces me to test it. ? RSPLUS1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 requir...
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multiple annotation in ChIPseeker
Nearest gene annotation Almost all annotation software calculate the distance of a peak to the nearest TSS and assign the peak to that gene. This can be misleading, as binding sites might be located between two start sites of different genes or hit different genes which have the same TSS location in the genome. The function annotatePeak provides ...
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