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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 ... [Read more...]

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

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 As pointed out in 'Are there too many biological databases', there is a problem that many out of date biological databases often don't ... [Read more...]

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/... [Read more...]

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 [Read more...]

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... [Read more...]

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 [Read more...]

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 ... [Read more...]

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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 ... [Read more...]

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 ... [Read more...]

Recently, there are some comments said that sometimes clusterProfiler failed in KEGG enrichment analysis. kaji331 compared cluserProfiler with GeneAnswers and found that clusterProfiler gives larger p values. The result forces me to test it. Read More: 251 Words Totally [Read more...]

In PLOB's QQ group, someone asked how to change the color of enrichment map in Cytoscape. I am very curious how enrichment map can helps to interpret enrichment results. It took me 2 hours to implement it using R and I am surprised that the enrichment map is better than anticipated. ... [Read more...]

去年ubuntu下apt-get了R-3.0.2, 用了没多久就发现了system命令有问题，通常情况下调用系统命令是正常的，但是我调用bowtie的时候，就会报错： Warning: Could not open read file "/tmp/8156.inpipe1" for reading; skipping... Read More: 2553 Words Totally [Read more...]

After two weeks developed, I have added/updated some plot functions in ChIPseeker (version __=1.0.1). ChIP peaks over Chromosomes Read More: 936 Words Totally [Read more...]

ChIPpeakAnno WAS the only one R package for ChIP peak annotation. I used it for annotating peak in my recent study. I found it does not consider the strand information of genes. I reported the bug to the authors, but they are reluctant to change. Read More: 2903 Words Totally [Read more...]

I used R package ChIPpeakAnno for annotating peaks, and found that it handle the DNA strand in the wrong way. Maybe the developers were from the computer science but not biology background. ?View Code RSPLUS1 Read More: 2754 Words Totally [Read more...]

Emacs is a great front-end for most of the command line tools. Although R-Studio is pretty good, I think Emacs/ESS is better. I’ve always used Emacs/ESS to run R, since 2007 on Ubuntu, on Windows, and on my MacBook Pro. It gives me the same experiences across all ... [Read more...]