[Bioc 3.5] NEWS of my BioC packages

I have 8 packages published within the Bioconductor project.

• ChIPseeker
• clusterProfiler
• DOSE
• ggtree
• GOSemSim
• meshes
• ReactomePA
• treeio

A new package treeio was included in BioC 3.5 release.

ChIPseeker

Bug fixed of intron rank and optimized getGeneAnno function.

clusterProfiler

1. Defined simplify generics as it was removed from IRanges.
2. enrichGO now supports ont="ALL" and will test three GO ontologies simultaneously.
3. dotplot for compareClusterResult not supports three GO sub-ontologies.
4. bitr_kegg supports converting Path/Module to geneID and vice versa.
5. plotGOgraph supports gseGO output by using core enriched gene.
6. see the updates of DOSE for other updates.

DOSE

• Now user can use options(mc.cores=x) to specify x cores for GSEA analysis.
• throw more friendly error msg if setReadable function fail to determine setType automatically.
• Call grid.newpage in gseaplot only if dev.interactive() is TRUE.
• dotplot now supports gseaResult.
• Output expected sample gene ID (sample from background) when input gene ID type not match.

ggtree

Now ggtree was splitted to treeio for tree input and output, and ggtree for tree visualization and annotation.

• facet_plot supports ggbio::geom_alignment.
• support setting x axis limits of Tree panel via xlim_tree.
• xlim_expand for setting x axis limits of any specific panel.
• revts for reverse time scale.
• groupOTU method now accept ‘overlap = c(“overwrite”, “origin”, “abandon”)’ parameter
• 2-dimensional tree layout supports phylo4d object
• aes(subset) now support logical vector contains NA
• supports parse=“emoji” in geom_cladelabel, geom_text2, geom_label2, geom_tiplab, geom_tiplab2
• unrooted layout now supports ‘daylight’ algorithm

GOSemSim

only documentation update.

meshes

no update

ReactomePA

only documentation update.

treeio

• defined new tree class treedata.
• as.treeedata.ggtree can convert ggtree output to treedata object.
• as.phylo.ggtree can convert ggtree output to phylo object.
• as.treedata.phylo4 & as.treedata.phylo4d for converting phylo4 and phylo4d object to treedata object.
• read.beast now also supports MrBayes output
• read.newick for parsing node.label as support values.
• drop.tip method for `treedata object.

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.