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.

clusterProfiler

Enrichment results may contains terms that are very general (less informative) and we do not want to use them. In this release, we provide dropGO function that can be used to drop selected GO terms or specific level of GO terms. It can be applied to output from both enrichGO and compareCluster. This is a feature request from @ahorvath.

Another feature request is to visualize GO enrichment result with GO topology. I implement plotGOgraph function by extending topGO to support output of both enrichGO or gseGO.

dotplot is another feature request and was implemented in DOSE as a general function for visualize enrichment result. clusterProfiler import this function.

merge_result function was implemented for merging enrichment results and then the results can be visualized simultaneously for comparison. This function was developed for comparing functional enrichment of GTEx paper. An example of comparing results from clusterProfiler and DAVID can be found in github.

A section ‘Functional analysis of NGS data’ was added in the vignette. The blog post illustrated using enricher and GSEA function to analyze user defined annotation.

DOSE

Network of Cancer Genes data was updated to version 4.9.0, contributed by @dalloliogm.

dotplot function was implemented for visualizing enrichment result and was imported to clusterProfiler and ReactomePA.

With new release of ChIPseeker, DOSE can be applied to NGS data.

Several bugs were removed and small improvement were incorporated.

ReactomePA

Now fly (Drosophila melanogaster) is supported.

viewPathway supports other organisms, which was contributed by @vladpetyuk.

Import dotplot from DOSE and add ‘Pathway analysis of NGS data’ section in vignette.

ChIPseeker

Implement seq2gene function for linking genomic regions to genes by many-to-many mapping. With this function, enrichment analysis of clusterProfiler, DOSE and ReactomePA can be applied to NGS data.

upsetplot function is implemented for viewing overlap of ChIP annotation.

Better implementation of internal function getFirstHitIndex contributed by @hpages. Now annotating a BED file of size about 1GB only take several minutes.

An issue of BED file that using the 0-based coordinate system was fixed.

GEO data information was updated, now ChIPseeker contains more than 18,000 BED file information. User can compare their own data with those deposited in GEO to identify co-occurrence binding proteins that maybe cooperated with the one we are interested in.

ggtree

My major focus in the past half year is on developing ggtree. ggtree has a lot of changes. Some of the updates can be found in Bioconductor Newsletter (Oct. 2015). In addition, I would like to emphasize the subview function which works fine with all the ggplot objects and was applied to plot pie graph on a map.

ggtree can be fun by using symbolic fonts, cartoonize the tree or annotating the tree with emoji.

There are many updates that based on the github version of ggplot2. Since the new features of ggplot2 are currently not available in CRAN. I do not commit the change to Bioconductor and will introduce these new feature to ggtree user when new version of ggplot2 is available in CRAN.

Citation

Yu G, Wang LG and He QY*. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383.

Yu G, Wang L, Han Y and He Q*. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.

G Yu, LG Wang, GR Yan, QY He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609.

G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. doi:10.1111/2041-210X.12628.

Yu G†, Li F†, Qin Y, Bo X*, Wu Y and Wang S*. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics. 2010, 26(7):976-978.

G Yu, QY He*. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems 2016, 12(2):477-479.