Blog Archives

dotplot for enrichment result

June 22, 2015
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dotplot for enrichment result

This is a feature request from clusterProfiler user. It's similar to what I implemented in clusterProfiler for comparing biological themes. For comparing different enrichment results, the x-axis represent different gene clusters while for a single enrichment result, the x-axis can be gene count or gene ratio. This is actually similar to traditional barplot, with dot position as bar height...

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ggtree with funny fonts

June 12, 2015
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ggtree with funny fonts

showtext is a neat solution to use various types of fonts in R graphs and make it easy to use funny fonts. With showtext, we can draw phylogenetic tree with different types of fonts even with symbolic/icon fonts. Read More: 638 Words Totally

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BMC favors source code plagiarism

May 27, 2015
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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. Read More: 9738...

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use clusterProfiler as an universal enrichment analysis tool

May 11, 2015
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use clusterProfiler as an universal enrichment analysis tool

clusterProfiler supports enrichment analysis of both hypergeometric test and gene set enrichment analysis. It internally support Gene Ontology analysis of about 20 species, Kyoto Encyclopedia of Genes and Genomes (KEGG) with all species that have annotation available in KEGG database, DAVID annotation, Disease Ontology and Network of Cancer Genes (via DOSE for human) and Reactome Pathway (via ReactomePA for...

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using GOSemSim to rank proteins obtained by co-IP

May 4, 2015
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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...

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NEWS of my BioC packages

April 20, 2015
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NEWS of my BioC packages

GOSemSim 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. clusterProfiler Read More: 2385 Words Totally

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an example of drawing beast tree using ggtree

March 31, 2015
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an example of drawing beast tree using ggtree

FigTree is designed for viewing beast output as demonstrated by their example data: BEAST output is well supported by ggtree and it's easy to reproduce such a tree view. ggtree supports parsing beast output by read.beast function. We can visualize the tree directly by using ggtree function. Since this is a time scale tree, we can set the parameter time_scale...

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DAVID functional analysis with clusterProfiler

March 16, 2015
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DAVID functional analysis with clusterProfiler

clusterProfiler was used to visualize DAVID results in a paper published in BMC Genomics. Some users told me that they may want to use DAVID at some circumstances. I think it maybe a good idea to make clusterProfiler supports DAVID, so that DAVID users can use visualization functions provided by clusterProfiler. Read More: 1642 Words...

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

February 28, 2015
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DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis

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 biologists to explore the similarities of diseases and of gene functions...

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

February 9, 2015
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[ggtree] updating a tree view using %<% operator

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

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