Blog Archives

an example of drawing beast tree using ggtree

March 31, 2015
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an example of drawing beast tree using ggtree

FigTree is designed for viewing beast output as demonstrated by their example data: BEAST output is well supported by ggtree and it's easy to reproduce such a tree view. ggtree supports parsing beast output by read.beast function. We can visualize the tree directly by using ggtree function. Since this is a time scale tree, we can set the parameter time_scale...

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DAVID functional analysis with clusterProfiler

March 16, 2015
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DAVID functional analysis with clusterProfiler

clusterProfiler was used to visualize DAVID results in a paper published in BMC Genomics. Some users told me that they may want to use DAVID at some circumstances. I think it maybe a good idea to make clusterProfiler supports DAVID, so that DAVID users can use visualization functions provided by clusterProfiler. Read More: 1642 Words...

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DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis

February 28, 2015
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DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis

My R/Bioconductor package, DOSE, published in Bioinformatics. Summary: Disease ontology (DO) annotates human genes in the context of disease. DO is important annotation in translating molecular findings from high-throughput data to clinical relevance. DOSE is an R package providing semantic similarity computations among DO terms and genes which allows biologists to explore the similarities of diseases and of gene functions...

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[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 »