Publications by R on Guangchuang Yu

SIR Model of Epidemics

12.10.2014

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 infe...

2116 sym R (1741 sym/2 pcs) 2 img 1 tbl

Yearly Topic Trend in PubMed

03.11.2014

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 scr...

1942 sym R (103 sym/2 pcs) 2 img 1 tbl

proper use of GOSemSim

22.11.2014

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 ma...

2957 sym R (20193 sym/12 pcs) 2 img

auto-complete in ESS

07.12.2014

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 Related To leave a comment for the author, please follow the link and comment on their blog: YGC » R. R-bloggers.com offers daily e-mail updates about R ...

581 sym

viewing and annotating phylogenetic tree with ggtree

21.12.2014

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 injec...

790 sym

learn R wisdom with fortunes

05.01.2015

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...

1800 sym R (884 sym/5 pcs) 6 img 1 tbl

ggtree in Bioconductor 3.1

18.01.2015

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 vigne...

1183 sym

KEGG enrichment analysis with latest online data using clusterProfiler

01.02.2015

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-ser...

3654 sym R (5535 sym/7 pcs) 3 tbl

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

09.02.2015

I am very exciting that I have received very positive feedback from Ahmed Moustafa and Simon Frost. ggtree now has equipped with a lot of new features. This time, I would like to introduce the replace operator, % Suppose we have build a tree view using ggtree with multiple layers, we don’t need to run the code again to build a new tree view wi...

1796 sym R (741 sym/12 pcs) 16 img 6 tbl

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

28.02.2015

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 ...

2075 sym 4 img