R (>= 3.0.0), c3net, infotheo, igraph, Matrix, lattice
Implementation of the BC3NET algorithm for gene regulatory network inference (de Matos Simoes and Frank Emmert-Streib, Bagging Statistical Network Inference from Large-Scale Gene Expression Data, PLoS ONE 7(3): e33624, <doi:10.1371/journal.pone.0033624>).

Bias-Corrected Methods for Estimating the ROC Surface of
Continuous Diagnostic Tests
Khanh To Duc, with contributions from Monica Chiogna and Gianfranco Adimari
The bias-corrected estimation methods for the receiver operating characteristics
ROC surface and the volume under ROC surfaces (VUS) under missing at random (MAR)
assumption.
R(>= 2.15.0), nnet, rgl, boot, stats, utils, graphics,
parallel

Duc-Khanh To, with contributions from Monica Chiogna and Gianfranco Adimari

R(>= 3.5.0), nnet, rgl, boot, stats, utils, graphics, parallel

Advanced Analysis of B Cell Receptor Repertoire Data
Methods for advanced analysis of B cell receptor repertoire data, like gene usage, mutations, clones and diversity and their visualisation.
vegan, parallel, doParallel, foreach, gplots, R (>= 3.2.2)

vegan, parallel, doParallel, foreach, gplots, ineq
stats, utils, graphics, grDevices, knitr, rmarkdown, pander

Methods for advanced analysis of B cell receptor repertoire
data, like gene usage, mutations, clones, diversity, distance measures and
multidimensional scaling and their visualisation.
vegan, parallel, doParallel, foreach, gplots, ineq, ape,
stringdist, proxy, plotrix

vegan, parallel, doParallel, foreach, gplots, ineq, ape,
stringdist, proxy

c(person("Dayne L", "Filer",
role = c("aut", "cre"),
email = "dayne.filer@gmail.com"),
person("Emanuele", "Aliverti",
role = c("aut"),
email = "aliverti@stat.unipd.it"),
person("Jeff", "Tilson",
role = c("aut")),
person("Kirk C", "Wilhelmsen",
role = c("aut")),
person("David B", "Dunson",
role = c("aut")))
Implements the projected t-SNE method for batch correction of
high-dimensional data. Please see Aliverti et al. (2020)
<doi:10.1093/bioinformatics/btaa189> for more information.
data.table, batchelor, kBET, splatter, scater, knitr, lisi,
harmony, dlfUtils, xtable
Dayne L Filer [aut, cre],
Emanuele Aliverti [aut],
Jeff Tilson [aut],
Kirk C Wilhelmsen [aut],
David B Dunson [aut]