Blog Archives

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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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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modified wp-codebox to highlight R code as in Pretty-R

December 5, 2012
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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. Read more »

project euler: problem 62

December 3, 2012
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The cube, 41063625 (3453), can be permuted to produce two other cubes: 56623104 (3843) and 66430125 (4053). In fact, 41063625 is the smallest cube which has exactly three permutations of its digits which are also cube.Find the smallest cube for which exactly five permutations of its digits are cube. Read...

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project euler: problem 61

November 22, 2012
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Triangle, square, pentagonal, hexagonal, heptagonal, and octagonal numbers are all figurate (polygonal) numbers and are generated by the following formulae: Triangle P3,n=n(n+1)/2 1, 3, 6, 10, 15, ... Square P4,n=n2 ...

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