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:
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
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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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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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.
Before I write my own script, I found that there is a well written package, RISmed, that provides many functions to access the NCBI databases.
I write a wrapper function called getPubmedTrend, which import EUtilsSummary and QueryCount from RISmed, to track PubMed trend. Another function called plotPubmedTrend was also implemented for visualizing the trend. These two functions is available in my toy package, yplots.
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