Blog Archives

SIR Model of Epidemics

October 12, 2014
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SIR Model of Epidemics

The SIR model divides the population to three compartments: Susceptible, Infected and Recovered. If the disease dynamic fits the SIR model, then the flow of individuals is one direction from the susceptible group to infected group and then to the recovered group. All individuals are assumed to be identical in terms of their susceptibility to infection, infectiousness if infected...

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multiple annotation in ChIPseeker

October 1, 2014
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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. Read More:...

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why clusterProfiler fails

August 6, 2014
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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. Read More: 251 Words Totally

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enrichment map

August 3, 2014
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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. Read More: 423 Words Totally

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再不相信预编译的R

July 23, 2014
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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... Read More: 2553 Words Totally

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visualization methods in ChIPseeker

April 30, 2014
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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 Read More: 936 Words Totally

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ChIPseeker for ChIP peak annotation

April 13, 2014
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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. Read More: 2903 Words Totally

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Bug of R package ChIPpeakAnno

January 13, 2014
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Bug of R package ChIPpeakAnno

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 Read More: 2754 Words Totally

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Run remote R in Emacs with ESS

November 13, 2013
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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...

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project euler — problem 68

December 12, 2012
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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...

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