[Bioc 3.5] NEWS of my BioC packages

I have 8 packages published within the Bioconductor project.

A new package treeio was included in BioC 3.5 release.

[Bioc 34] NEWS of my BioC packages

I have 7 packages published within the Bioconductor project.

A new package meshes was included in BioC 3.4 release.

[Bioc 33] NEWS of my BioC packages

Today is my birthday and it happened to be the release day of Bioconductor 3.3. It’s again the time to reflect what I’ve done in the past year.

[Bioc 32] NEWS of my BioC packages

In BioC 3.2 release, all my packages including GOSemSim, clusterProfiler, DOSE, ReactomePA, and ChIPseeker switch from Sweave to R Markdown for package vignettes.


To make it consistent between GOSemSim and clusterProfiler, ‘worm’ was deprecated and instead we should use ‘celegans’. As usual, information content data was updated.

BMC favors source code plagiarism

I found source code plagiarism a year ago and reported this case to BMC Systems Biology:

I listed source code of many functions that are exactly copied from GOSemSim with only function name changed in my email. The detail of source code plagiarism can also be found at Proper use of GOSemSim.

using GOSemSim to rank proteins obtained by co-IP

Co-IP is usually used to identified interactions among specific proteins. It is widely used in detecting protein complex. Unfortunately, an identified protein may not be an interactor, and sometimes can be a background contaminant. Ranking proteins can help us to focus a study on a few high quality candidates for subsequent interaction investigation. My R package GOSemSim has been used in many studies to investigate protein protein interaction, see 1, 2, 3, 4 and more.

[Bioc 31] NEWS of my BioC packages


GOSemSim was first implemented in 2008 and published in Bioinformatics in 2010. It’s now a mature package with no bugs found in the past half year. Only vignette and Information content data were updated.

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.

GOSemSim an R package for measuring semantic similarity among GO terms and gene products


SUMMARY: The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. Four information content (IC)- and a graph-based methods are implemented in the GOSemSim package, multiple species including human, rat, mouse, fly and yeast are also supported. The functions provided by the GOSemSim offer flexibility for applications, and can be easily integrated into high-throughput analysis pipelines. AVAILABILITY: GOSemSim is released under the GNU General Public License within Bioconductor project, and freely available at http://bioconductor.org/packages/2.6/bioc/html/GOSemSim.html.