Blog Archives

auto-complete in ESS

December 7, 2014
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To support auto complete in Emacs, we need to install the auto-complete extension. To activate auto complete, we need to load it at Emacs startup. Read More: 440 Words Totally

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proper use of GOSemSim

November 22, 2014
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proper use of GOSemSim

One day, I am looking for R packages that can analyze PPI and after searching, I found the ppiPre package in CRAN. The function of this package is not impressive, and I already knew some related works, including http://intscore.molgen.mpg.de/. The authors of this webserver contacted me for the usages of GOSemSim when they developing it. Read more »

Yearly Topic Trend in PubMed

November 3, 2014
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Yearly Topic Trend in PubMed

I found an R script in R-blogger that can be used to track PubMed trend. The script needs Perl package TGen-EUtils to perform query and it is not available now. It's not difficult to query Pubmed record in R. We can use RCurl package to fetch and use XML package to parse the downloaded record as shown in stackoverflow.

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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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