Machine Learning-based Differential Network Analysis of
Transcriptome Data
R (>= 2.15.1), biwt, cairoDevice, e1071, fBasics,
GeneSelector, grDevices, gplots, gWidgets, gWidgetsRGtk2, hash,
igraph, nnet, parmigene, pROC, qvalue, ROCR, rsgcc, stringr,
snowfall
Functions necessary to perform the machine learning-based
differential network analysis of transcriptome data.

bigmemory, GeneSelector, gplots, nnet, cairoDevice, fBasics

Phase haplotypes from genotypes based on a list of known
haplotypes. Suited to highly diverse loci such as HLA.

Sacha Epskamp, Marie K. Deserno and Laura F. Bringmann
Compute estimates of the multivariate vector autoregression model as
used to (but not limited to) analyze experience sampling method data in
clinical psychology. The model can be extended through treatment effects,
covariates and pre- and post-assessment effects.

lme4, arm, qgraph, dplyr, clusterGeneration, mvtnorm, corpcor,
plyr, abind, methods
Compute estimates of the multivariate vector autoregression model as
introduced by Bringmann et al. (2013) which can be extended through treatment effects,
covariates and pre- and post-assessment effects.

Estimates the multi-level vector autoregression model on time-series data.
Three network structures are obtained: temporal networks, contemporaneous
networks and between-subjects networks.

lme4, arm, qgraph, dplyr, clusterGeneration, mvtnorm, corpcor,
plyr, abind, methods, parallel

lme4, arm, qgraph, dplyr, clusterGeneration, mvtnorm, corpcor,
plyr, abind, methods, parallel, MplusAutomation, graphicalVAR

lme4, arm, qgraph, dplyr (>= 0.5.0), clusterGeneration,
mvtnorm, corpcor, plyr, abind, methods, parallel,
MplusAutomation, graphicalVAR

lme4, arm, qgraph, dplyr, clusterGeneration, mvtnorm, corpcor,
plyr, abind, methods, parallel, MplusAutomation

lme4, arm, qgraph, dplyr (>= 0.5.0), clusterGeneration,
mvtnorm, corpcor, plyr, abind, methods, parallel,
MplusAutomation, graphicalVAR, rlang
c(
person("Sacha", "Epskamp", email = "mail@sachaepskamp.com",role = c("aut", "cre")),
person("Marie K.", "Deserno", role = c("aut")),
person("Laura F.", "Bringmann", role = c("aut")),
person("Myrthe", "Veenman", role = c("ctb")))
Sacha Epskamp [aut, cre],
Marie K. Deserno [aut],
Laura F. Bringmann [aut],
Myrthe Veenman [ctb]