Last data update: 2014.03.03
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genefu
Package: genefu
Type: Package
Title: Computation of Gene Expression-Based Signatures in Breast Cancer
Version: 2.4.2
Date: 2015-10-28
Description: Description: This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.
Author: Deena M.A. Gendoo, Natchar Ratanasirigulchai, Markus S. Schroder, Laia Pare, Joel S. Parker, Aleix Prat, and Benjamin Haibe-Kains
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>, Markus Schroeder <markus.schroeder@ucdconnect.ie>
biocViews: DifferentialExpression, GeneExpression, Visualization,
Clustering, Classification
Depends: survcomp, mclust, limma, biomaRt, iC10, AIMS, R (>= 2.10)
Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ,
breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT,
breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival
Imports: amap
VignetteBuilder: knitr
License: Artistic-2.0
URL: http://www.pmgenomics.ca/bhklab/software/genefu
LazyData: yes
NeedsCompilation: no
Packaged: 2016-05-16 02:51:30 UTC; biocbuild
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'genefu' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'genefu'
finding HTML links ... done
bimod html
boxplotplus2 html
claudinLow html
claudinLowData html
collapseIDs html
compare.proto.cor html
compute.pairw.cor.meta html
compute.pairw.cor.z html
compute.proto.cor.meta html
cordiff.dep html
endoPredict html
expos html
Rd warning: /tmp/RtmplNdtRK/R.INSTALL312e5de6593b/genefu/man/expos.Rd:23: missing file link 'data.expos'
fuzzy.ttest html
gene70 html
gene76 html
genefu-package html
geneid.map html
genius html
ggi html
ihc4 html
intrinsic.cluster html
intrinsic.cluster.predict html
map.datasets html
medianCtr html
mod1 html
mod2 html
modelOvcAngiogenic html
molecular.subtyping html
nkis html
Rd warning: /tmp/RtmplNdtRK/R.INSTALL312e5de6593b/genefu/man/nkis.Rd:23: missing file link 'data.nkis'
npi html
oncotypedx html
ovcAngiogenic html
ovcCrijns html
ovcTCGA html
ovcYoshihara html
overlapSets html
pam50 html
pik3cags html
power.cor html
ps.cluster html
read.m.file html
Rd warning: /tmp/RtmplNdtRK/R.INSTALL312e5de6593b/genefu/man/read.m.file.Rd:16: missing file link 'read.csv'
readArray html
rename.duplicate html
rescale html
rorS html
scmgene.robust html
scmod1.robust html
scmod2.robust html
setcolclass.df html
sig.endoPredict html
sig.gene70 html
sig.gene76 html
sig.genius html
sig.ggi html
sig.oncotypedx html
sig.pik3cags html
sig.score html
sig.tamr13 html
sigOvcAngiogenic html
sigOvcCrijns html
sigOvcSpentzos html
sigOvcTCGA html
sigOvcYoshihara html
spearmanCI html
ssp2003 html
ssp2006 html
st.gallen html
stab.fs html
stab.fs.ranking html
strescR html
subtype.cluster html
subtype.cluster.predict html
tamr13 html
tbrm html
vdxs html
Rd warning: /tmp/RtmplNdtRK/R.INSTALL312e5de6593b/genefu/man/vdxs.Rd:23: missing file link 'data.vdxs'
weighted.meanvar html
write.m.file html
Rd warning: /tmp/RtmplNdtRK/R.INSTALL312e5de6593b/genefu/man/write.m.file.Rd:22: missing file link 'read.csv'
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genefu)
Making 'packages.html' ... done
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