Tag Archives: R

ggtree in Bioconductor 3.1

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.

Now you can use the following command to install ggtree:

?View Code RSPLUS

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

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.

The fortune program provides UNIX related quotations, while the quotations supplied by the R package, fortunes, are all R related. We can learn a lot from these quotations.

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viewing and annotating phylogenetic tree with ggtree

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, but they are restricted to a few supported data types. It is hard/impossible to inject user specific data.

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auto-complete in ESS

Auto complete is good, it can save you times in typing and prevent typo sometimes.


RStudio now supports function arguments in auto complete. ESS's auto complete is more advance, it supports help page.

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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.

What makes me curious is that the ppiPre package can calculate GO semantic similarity and supports 20 species exactly like GOSemSim. I opened the source tarball, and surprisingly found that its sources related to semantic similarity calculation are totally copied from GOSemSim.

GOSemSim was firstly released in 2008 Bioconductor 2.4 (at that time, devel version) and published in Bioinformatics in 2010. After compared the sources, I found the sources in ppiPre were copied from GOSemSim version 1.6.8 which released in 2010 Bioconductor 2.6.
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