Evolution of the DECIPHER package

Originally presented at the BioC 2022 conference in Seattle, USA. 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. 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.