GOSemSim was first implemented in 2008 and published in Bioinformatics in 2010. It’s now a mature package with no bugs found in the past half year. Only vignette and Information content data were updated.
clusterProfiler was developed in 2011 and published in OMICS in 2012. I am very glad to find that clusterProfiler was presented in the book ‘Bioinformatics with R Cookbook‘: In this release, KEGG enrichment analysis (both hypergeometric and GSEA) now supports using latest online data and DAVID functional analysis is also supported. In addition, compareCluster function now supports formula interface like x ~ y + z; this feature was contributed by @dalloliogm. Considering that many new users have problem of converting biological IDs, clusterProfiler contains a new function bitr, stands for Biological Id TranslatoR. NOW, clusterProfiler is not restricted to GO and KEGG analyses. All kinds of annotation can be supported via enricher function for hypergeometric test and GSEA function for gene set enrichment analysis. These two functions are not yet documented in vignette and will soon.
DOSE was first released in 2011, and has been published in Bioinformatics on February 2015. An example of applying DOSE for disease ontology enrichment analysis can be found in Genome-wide Identification and Characterization of Fixed Human-Specific Regulatory Regions. Besides, DOSE also supports Network of Cancer Genes database.
ReactomePA was developed in 2012 when KEGG is no longer available in public domain. In BioC 3.0, reactome.db has a lot of issues. Until the early of this April, Bioconductor restored reactome.db in Bioc 3.0 to Bioc 2.14. This issue affects ReactomePA several months and was removed in BioC 3.1.
ChIPseeker was developed in 2014, after I found a bug of ChIPpeakAnno package. Many new features were added thereafter, including several visualization methods, multiple annotations, ChIP-peak comparison and data mining with GEO database. ChIPseeker has been published in Bioinformatics. In this release, several minor bugs were fixed, a new parameter genomicAnnotationPriority was added in annotatePeak and plotAvgProf supports estimating confidence interval as shown below: This CI estimation feature was contributed by Yan Yun. ChIPseeker works fine with other ChIP-seq related tools as demonstrated in the ChIPseq Analysis workflow. It has also been presented in 2014 CSHLseq course and 2015 Use Bioconductor course.
ggtree was developed on December 2014, when I got tired of annotating tree by modifying node labels. This release (version=1.0.0) is the first release, output of many common software in evolution were supported and many new features were introduced in the past few months. Please view the vignette to find out more and I can guarantee that you won’t be disappointed.
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.
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.