Integrative Inference of De Novo Cis-Regulatory Modules
c(person("Xi", "Chen", email = "xichen86@vt.edu", role = c("aut", "cre")),
person("Jianhua", "Xuan", email = "xuan@vt.edu", role = "aut"))
Prior transcription factor binding knowledge and target gene expression data are integrated in a Bayesian framework for functional cis-regulatory module inference. Using Gibbs sampling, we iteratively estimate transcription factor associations for each gene, regulation strength for each binding event and the hidden activity for each transcription factor.

Tools for Accessing the Botanical Ecology and Information
Network Database
person("Brian", "Maitner", email = "bmaitner@gmail.com", role = c("aut", "cre"))
Provides Tools for Accessing the Botanical Information and Ecology Network Database.  The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data (See <http://Bien.nceas.ucsb.edu/Bien/> for more Information).  This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.
maptools, rgeos, rgdal, sp, DBI, ape, methods

Tools for Accessing the Botanical Information and Ecology
Network Database
Provides Tools for Accessing the Botanical Information and Ecology Network Database.  The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data (See <http://Bien.nceas.ucsb.edu/bien/> for more Information).  This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.

knitr, rmarkdown, testthat, maptools, maps

rgeos, rgdal, sp, DBI, ape, methods, sf, fasterize, raster,
doParallel, parallel, foreach

Provides Tools for Accessing the Botanical Information and Ecology Network Database.  The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data (See <https://bien.nceas.ucsb.edu/bien/> for more Information).  This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.