Tag Archives: R

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

My R/Bioconductor package, DOSE, published in Bioinformatics.

DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
G Yu, LG Wang, GR Yan, QY He.
Bioinformatics 2015, 31(4):608-609
Received: 7 May 2014
Accepted: 14 October 2014
Online: 17 October 2014
DOI: 10.1093/bioinformatics/btu684

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 in disease perspective. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented to support discovering disease associations of high-throughput biological data. This allows biologists to verify disease relevance in a biological experiment and identify unexpected disease associations. Comparison among gene clusters is also supported.

Availability and implementation: DOSE is released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/release/bioc/html/DOSE.html).

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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.

ggtree now has equipped with a lot of new features. This time, I would like to introduce the replace operator, %<%.

Suppose we have build a tree view using ggtree with multiple layers, we don't need to run the code again to build a new tree view with another tree. In ggtree, we provides an operator, %<%, for updating tree view.

?View Code RSPLUS
ggtree(rtree(15)) %< % rtree(30)

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KEGG enrichment analysis with latest online data using clusterProfiler

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 get offline. This issue also exists in web-server or software that using out-of-date data. For example, the WEGO web-server stopped updating GO annotation data since 2009, and WEGO still online with many people using it. The biological story may changed totally if using a recently updated data. Seriously, We should keep an eye on this issue.

Now enrichKEGG function is reloaded with a new parameter use_internal_data. This parameter is by default setting to FALSE, and enrichKEGG function will download the latest KEGG data for enrichment analysis. If the parameter use_internal_data is explicitly setting to TRUE, it will use the KEGG.db which is still supported but not recommended.

With this new feature, supported species is unlimited if only there are KEGG annotations available in KEGG database. You can access the full list of species supported by KEGG via: http://www.genome.jp/kegg/catalog/org_list.html
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ggtree in Bioconductor 3.1

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.

Now you can use the following command to install ggtree:

?View Code RSPLUS
                 repos = "http://www.bioconductor.org/packages/devel/bioc",
                 type  = "source")

Find out more at http://www.bioconductor.org/packages/3.1/bioc/html/ggtree.html and check out the vignette, http://www.bioconductor.org/packages/3.1/bioc/vignettes/ggtree/inst/doc/ggtree.html

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