Blog Archives

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 RSPLUS1Read 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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project-euler–problem 65

September 16, 2012
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The square root of 2 can be written as an infinite continued fraction.\( \sqrt{2} = 1+\frac{1}{2+\frac{1}{2+\frac{1}{2+\frac{1}{2+?}}}} \) \sqrt{2} = 1+\frac{1}{2+\frac{1}{2+\frac{1}{2+\frac{1}{2+?}}}}The infinite continued fraction can be written, √2 = , (2) indicates that 2 repeats ad infinitum. In a similar way, √23 = .Read More: 1030 Words Totally

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clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

May 6, 2012
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Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently,...

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draw chinese character Jiong using ggplot2

February 17, 2012
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draw chinese character Jiong using ggplot2

The Chinese character Jiong (囧) is now widely used for expressing ideas or feelings such as annoyance, shock, embarrassment, awkwardness, scorn.The function plot of y=1/(x^2-1) looks very similar of this symbol.I use ggplot2 to draw the symbol of Jiong.Read More: 359 Words Totally

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ML-Class Ex 7 – kMeans clustering

December 24, 2011
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ML-Class Ex 7 – kMeans clustering

The K-means algorithm is a method to automatically cluster similar data examples together.The intuition behind K-means is an iterative procedure that starts by guessing the initial centroids, and then refines this guess by repeatedly assigning examples to their closest centroids and then recomputing the centroids based on the assignments.Read more »