Blog Archives

[ggtree] updating a tree view using %<% operator

February 9, 2015
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[ggtree] updating a tree view using %<% operator

I am very exciting that I have received very positive feedback from Ahmed Moustafa and Simon Frost. Read More: 401 Words Totally

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KEGG enrichment analysis with latest online data using clusterProfiler

February 1, 2015
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KEGG.db is not updated since 2012. The data is now pretty old, but many of the Bioconductor packages still using it for KEGG annotation and enrichment analysis. As pointed out in 'Are there too many biological databases', there is a problem that many out of date biological databases often don't get offline. This issue also exists in web-server or software...

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ggtree in Bioconductor 3.1

January 18, 2015
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I am very glad that ggtree is now available via Bioconductor. This is my 6th Bioconductor package. ggtree now supports parsing output files from BEAST, PAML, HYPHY, EPA and PPLACER and can annotate phylogenetic tree directly using plot methods. Find out more at http://www.bioconductor.org/packages/3.1/bioc/html/ggtree.html and check out the vignette, http://www.bioconductor.org/packages/3.1/bioc/vignettes/ggtree/inst/doc/ggtree.html Read More: 387 Words Totally

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learn R wisdom with fortunes

January 5, 2015
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learn R wisdom with fortunes

I like running fortune every time when the terminal was started. A screenshot is shown below: At the end of the post trick things in R, I introduced the fortunes package of R. Read More: 1656 Words Totally

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viewing and annotating phylogenetic tree with ggtree

December 21, 2014
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When I need to annotate nucleotide substitutions in the phylogenetic tree, I found that all the software are designed to display the tree but not annotating it. Some of them may support annotating the tree with specific data such as bootstrap values, b...

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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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