Last data update: 2014.03.03
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nethet
Package: nethet
Type: Package
Title: A bioconductor package for high-dimensional exploration of
biological network heterogeneity
Version: 1.4.2
Date: 2015-08-18
Author: Nicolas Staedler, Frank Dondelinger
Maintainer: Nicolas Staedler <staedler.n@gmail.com>,
Frank Dondelinger <fdondelinger.work@gmail.com>
Description: Package nethet is an implementation of statistical solid
methodology enabling the analysis of network heterogeneity from
high-dimensional data. It combines several implementations of recent
statistical innovations useful for estimation and comparison of networks in
a heterogeneous, high-dimensional setting. In particular, we provide code
for formal two-sample testing in Gaussian graphical models (differential
network and GGM-GSA; Stadler and Mukherjee, 2013, 2014) and make a novel
network-based clustering algorithm available (mixed graphical lasso,
Stadler and Mukherjee, 2013).
Imports: glasso, mvtnorm, parcor, GeneNet, huge, CompQuadForm, ggm,
mclust, parallel, GSA, limma, multtest, ICSNP, glmnet, network,
ggplot2
Suggests: knitr, xtable, BiocStyle
biocViews: Clustering, GraphAndNetwork
VignetteBuilder: knitr
License: GPL-2
Packaged: 2016-05-16 05:06:51 UTC; biocbuild
NeedsCompilation: yes
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'nethet' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c betamat_diffnet.c -o betamat_diffnet.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o nethet.so betamat_diffnet.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/nethet/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'nethet'
finding HTML links ... done
EXPStep.mix html
MStepGlasso html
NetHet-package html
agg.pval html
agg.score.iriz.scale html
agg.score.iriz.shift html
aggpval html
aic.glasso html
beta.mat html
beta.mat.diffregr html
bic.glasso html
buildDotPlotDataFrame html
bwprun_mixglasso html
cv.fold html
cv.glasso html
diffnet_multisplit html
diffnet_pval html
diffnet_singlesplit html
diffregr_multisplit html
diffregr_pval html
diffregr_singlesplit html
dot_plot html
error.bars html
est2.my.ev2 html
est2.my.ev2.diffregr html
est2.my.ev3 html
est2.my.ev3.diffregr html
est2.ww.mat.diffregr html
est2.ww.mat2 html
est2.ww.mat2.diffregr html
export_network html
func.uinit html
generate_2networks html
generate_inv_cov html
getinvcov html
ggmgsa_multisplit html
ggmgsa_singlesplit html
glasso.invcor html
glasso.invcov html
glasso.parcor html
gsea.highdimT2 html
gsea.iriz html
gsea.iriz.scale html
gsea.iriz.shift html
gsea.t2cov html
het_cv_glasso html
hugepath html
inf.mat html
invcov2parcor html
invcov2parcor_array html
lambda.max html
lambdagrid_lin html
lambdagrid_mult html
loglik_mix html
logratio html
logratio.diffregr html
make_grid html
mcov html
mixglasso html
mixglasso_init html
mixglasso_ncomp_fixed html
mle.ggm html
my.ev2.diffregr html
my.p.adjust html
my.ttest html
my.ttest2 html
mytrunc.method html
perm.diffregr_pval html
perm.diffregr_teststat html
plot.diffnet html
plot.diffregr html
plot.ggmgsa html
plot.nethetclustering html
plotCV html
plot_2networks html
print.nethetsummary html
q.matrix.diffregr html
q.matrix.diffregr3 html
q.matrix.diffregr4 html
q.matrix3 html
q.matrix4 html
scatter_plot html
screen_aic.glasso html
screen_bic.glasso html
screen_cv.glasso html
screen_cv1se.lasso html
screen_cvfix.lasso html
screen_cvmin.lasso html
screen_cvsqrt.lasso html
screen_cvtrunc.lasso html
screen_full html
screen_lasso html
screen_mb html
screen_mb2 html
screen_shrink html
shapiro_screen html
sim_mix html
sim_mix_networks html
sparse_conc html
summary.diffnet html
summary.diffregr html
summary.ggmgsa html
summary.nethetclustering html
sumoffdiag html
symmkldist html
t2cov.lr html
t2diagcov.lr html
test.sd html
test.t2 html
tr html
twosample_single_regr html
w.kldist html
ww.mat html
ww.mat.diffregr html
ww.mat2 html
ww.mat2.diffregr html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (nethet)
Making 'packages.html' ... done
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