Blog Archives

R kernel in Jupyter notebook 3

November 29, 2015
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R kernel in Jupyter notebook 3

I followed the post, Installing an R kernel for IPython/jupyter notebook 3 on OSX, to install jupyter with python3 and R kernels in my iMac. I have elementaryOS on my Macbook Pro and also want to have jupyter on it. The installation process is quite similar. Read More: 824 Words Totally

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phylomoji with ggtree

November 8, 2015
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phylomoji with ggtree

If you search the hashtag, #phylomoji, in twitter, you can find many creative phylogenetic tree constructed with emoji. #phylomoji with Darwin's water bears! @OxyEvo 🌱 🐟 🐻 🐋 | | |_____| ...

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Comparison of clusterProfiler and GSEA-P

November 2, 2015
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Comparison of clusterProfiler and GSEA-P

Thanks @mevers for raising the issue to me and his efforts in benchmarking clusterProfiler. He pointed out two issues: Read More: 2944 Words Totally

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use simplify to remove redundancy of enriched GO terms

October 21, 2015
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use simplify to remove redundancy of enriched GO terms

To simplify enriched GO result, we can use slim version of GO and use enricher function to analyze. Another strategy is to use GOSemSim to calculate similarity of GO terms and remove those highly similar terms by keeping one representative term. To make this feature available to clusterProfiler users, I develop a simplify method to reduce redundant GO terms from...

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[BioC 3.2] NEWS of my BioC packages

October 15, 2015
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In BioC 3.2 release, all my packages including GOSemSim, clusterProfiler, DOSE, ReactomePA, and ChIPseeker switch from Sweave to R Markdown for package vignettes. GOSemSim To make it consistent between GOSemSim and clusterProfiler, 'worm' was deprecated and instead we should use 'celegans'. As usual, information content data was updated. Read More: 2984 Words...

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ChIPseq data mining with ChIPseeker

October 1, 2015
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ChIPseq data mining with ChIPseeker

ChIP-seq is rapidly becoming a common technique and there are a large number of dataset available in the public domain. Results from individual experiments provide a limited understanding of chromatin interactions, as there is many factors cooperate to regulate transcription. Unlike other tools that designed for single dataset, ChIPseeker is designed for comparing profiles of ChIP-seq datasets at different...

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subsetting data in ggtree

September 23, 2015
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subsetting data in ggtree

Subsetting is commonly used in ggtree as we would like to for example separating internal nodes from tips. We may also want to display annotation to specific node(s)/tip(s). Some software may stored clade information (e.g. bootstrap value) as internal node labels. Indeed we want to manipulate such information and taxa labels separately. Read More: 962 Words...

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comic phylogenetic tree with ggtree and comicR

September 7, 2015
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comic phylogenetic tree with ggtree and comicR

ggtree applies the concepts of grammar of graphic in phylogenetic tree presentation and make it easy to add multiple layers of text and even figures above a 🌲. Here, I cartoonize a phylogenetic tree generated by ggtree with comicR, which is a funny package to generate comic (xkcd-like) graph in R. Have fun with ggtree and comicR. Read more »

embeding a subplot in ggplot via subview

August 30, 2015
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embeding a subplot in ggplot via subview

I implemented a function, subview, in ggtree that make it easy to embed a subplot in ggplot. An example is shown below: Read More: 131 Words Totally

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functional enrichment analysis with NGS data

August 20, 2015
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functional enrichment analysis with NGS data

I found that there is a Bioconductor package, seq2pathway, that can apply functional analysis to NGS data. It consists of two components, seq2gene and gene2pathway. seq2gene converts genomic coordination to genes while gene2pathway performs functional analysis at gene level. Read More: 1007 Words Totally

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