Evolution Of The DECIPHER Package For Comparative Genomics
Author(s): Erik Scott Wright
Affiliation(s): University of Pittsburgh
The DECIPHER package has been part of Bioconductor for about 11 years and has continued to grow in scope and utility. Although the R package was originally developed for designing oligonucleotide probes and primers, it now includes cutting-edge functionality for multiple sequence alignment, sequence classification, phylogenetics, and many other advanced applications of bioinformatics. Here, I will describe the evolution of DECIPHER's focus and abilities. I will touch on the inclusion of advanced features such as OpenMP for multi-threading and SIMD for even greater parallelism. I will discuss the intrinsic challenges and opportunities associated with developing, expanding, and supporting large-scale tools within the R environment. Also, I will describe how DECIPHER has performed on published benchmarks used to characterize different parts of its functionality. DECIPHER's journey from a new Bioconductor package to one with tens-of-thousands of users is ongoing, and this presentation will highlight the past, present, and future of this unique package.