Evolution Of The DECIPHER Package For Comparative Genomics
Channel: R Consortium
Date: 2022-08-29

Eric Wright, Ph.D., with the department of Biomedical Informatics at the University of Pittsburgh, presented a short talk at the Bioconductor Conference 2022. Dr. Wright gave his presentation on the Evolution of the DECIPHER package for comparative genomics.   

The DECIPHER package has been part of Bioconductor for about 11 years and has continued to grow in scope and utility. Although this 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. In the presentation, Dr. Wright describes the evolution of DECIPHER's focus and abilities. He touched on the inclusion of advanced features such as OpenMP for multi-threading and SIMD for even greater parallelism. Furthermore, Dr. Wright discussed the intrinsic challenges and opportunities associated with developing, expanding, and supporting large-scale tools within the R environment. Dr. Wright also described 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 highlighted the past, present, and future of this unique package.

Main Sections

0:00 Introduction 
0:30 Guiding inspiration is to empower users 
1:29 DECIPHER design philosophy 
4:38 Evolution of the DECIPHER package 
9:37 Summary of the DECIPHER design philosophy
10:15 Independent validation of alignments 
10:57 AssessORF: gene caller benchmark 
11:43 Exponential growth in available genomes
12:06 Growth of DECIPHER in code
13:26 Exponential growth in DECIPHER users
13:55 Acknowledgements
14:30 Q&A

More Resources 

Bioconductor Conference Site: https://bioc2022.bioconductor.org/ 
BioC2022 Github: https://github.com/Bioconductor/BioC2022 

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