Publications by R on Guangchuang Yu
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. ?View Code RSPLUS1 2 3 4 5 6 req...
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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 param...
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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 investigat...
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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...
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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. I got reply from the Editor 3 days after (see screensh...
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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. ?View Code RSPLUS1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 require(showtext) font.add.google("Goch...
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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 traditi...
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flip and rotate branches in ggtree
flip function is a feature request from ggtree user. It accepts a tree view and two node numbers and exchange the positions of the selected clades. ?View Code RSPLUS1 2 3 4 5 require(ggtree) set.seed(2015-07-01) tr <- rtree(30) p <- ggtree(tr) + geom_text(aes(label=node)) gridExtra::grid.arrange(p, flip(p, 38, 33), ncol=2) It's chainable and all...
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ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization
My R/Bioconductor package, ChIPseeker, published in Bioinformatics. ChIPseeker had been cited by http://www.biomedcentral.com/1471-2164/16/292 and http://www.jbc.org/content/early/2015/06/18/jbc.M115.668558.short, and was used (not cited) in http://nar.oxfordjournals.org/content/early/2015/06/27/nar.gkv642.abstract and http://emboj.embopress.org/...
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[paper published] ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization
My R/Bioconductor package, ChIPseeker, published in Bioinformatics. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization G Yu, LG Wang, QY He. Bioinformatics 2015, 31(14):2382-2383 DOI: 10.1093/bioinformatics/btv145 Summary: ChIPseeker is an R package for annotating ChIP-seq data analysis. It supports ann...
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