DepEst: an R package of important dependency estimators for gene network inference algorithms

Abstract

Abstract Gene network inference algorithms (GNI) are popular in bioinformatics area. In almost all GNI algorithms, the main process is to estimate the dependency (association) scores among the genes of the dataset. We present a bioinformatics tool, DepEst (Dependency Estimators), which is a powerful and flexible R package that includes 11 important dependency score estimators that can be used in almost all GNI Algorithms. DepEst is the first bioinformatics package that includes such a large number of estimators that runs both in parallel and serial. DepEst is currently available at https://github.com/altayg/Depest. Package access link, instructions, various workflows and example data sets are provided in the supplementary file.