networkBMA: Regression-based network inference using Bayesian Model Averaging

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An extension of Bayesian Model Averaging (BMA) for network construction using time series gene expression data. Includes assessment functions and sample test data.

Author
Chris Fraley, Wm. Chad Young, Ling-Hong Hung, Kaiyuan Shi, Ka Yee Yeung, Adrian Raftery (with contributions from Kenneth Lo)
Date of publication
None
Maintainer
Ka Yee Yeung <kayee@u.washington.edu>
License
GPL (>= 2)
Version
2.12.0

View on Bioconductor

Man pages

contabs
Contingency tables for networks with probabilistic edges.
contabs.netwBMA
Network assessment with incomplete context.
contabs.prelim
Preliminary calculation for network assessment.
dream4
DREAM 4 (Stolovitsky et al. 2007) 'gold standard' reference...
fastBMAcontrol
Control parameters for 'networkBMA' when using fastBMA...
fastgControl
Control parameters for using Zellner's g-prior in fastBMA...
gControl
Control parameters for using Zellner's g-prior in 'ScanBMA'
iBMAcontrolLM
Control parameters for 'iterateBMAlm'
iterateBMAlm
Iterative BMA for linear modeling with prior variable...
networkBMA
Gene network inference from time series data via BMA.
networkBMA-internal
Internal functions for the networkBMA package
roc
Receiver Operating Characteristic and Precision-Recall Curves
ScanBMA
Bayesian Model Averaging for linear regression models.
ScanBMAcontrol
Control parameters for 'ScanBMA'
scores
Scores for assessment from contingency tables.
summary.networkBMA
Summarizes a 'networkBMA' object.
varord
Variable orderings for linear regression.
vignette
The subsets of the yeast-rapamycin time-series data from...
writeEdges
Output network edges to text in Cytoscape-readable format.

Files in this package

networkBMA/DESCRIPTION
networkBMA/NAMESPACE
networkBMA/NEWS
networkBMA/R
networkBMA/R/FastScanBMABIC.r
networkBMA/R/FastScanBMAg.r
networkBMA/R/RcppExports.R
networkBMA/R/ScanBMA.R
networkBMA/R/ScanBMABIC.r
networkBMA/R/ScanBMAcontrol.R
networkBMA/R/ScanBMAg.r
networkBMA/R/bicreg.pr.R
networkBMA/R/bicreg.pr.resid.R
networkBMA/R/contabs.R
networkBMA/R/contabs.netwBMA.R
networkBMA/R/contabs.prelim.R
networkBMA/R/fastBMA.R
networkBMA/R/fastBMAcontrol.R
networkBMA/R/iBMAcontrolLM.R
networkBMA/R/iterateBMAlm.R
networkBMA/R/iterateBMAlm.resid.R
networkBMA/R/list2df.R
networkBMA/R/matrixFormat.R
networkBMA/R/networkBMA.R
networkBMA/R/prc.R
networkBMA/R/refNetwCalc.R
networkBMA/R/roc.R
networkBMA/R/scores.R
networkBMA/R/summary.networkBMA.R
networkBMA/R/varord.R
networkBMA/R/writeEdges.R
networkBMA/build
networkBMA/build/vignette.rds
networkBMA/data
networkBMA/data/datalist
networkBMA/data/dream4.rda
networkBMA/data/vignette.rda
networkBMA/include
networkBMA/include/cblas.h
networkBMA/include/lapacke.h
networkBMA/include/lapacke_config.h
networkBMA/include/lapacke_mangling.h
networkBMA/include/lapacke_utils.h
networkBMA/inst
networkBMA/inst/CITATION
networkBMA/inst/cite
networkBMA/inst/doc
networkBMA/inst/doc/networkBMA.R
networkBMA/inst/doc/networkBMA.Rnw
networkBMA/inst/doc/networkBMA.pdf
networkBMA/inst/unitTests
networkBMA/man
networkBMA/man/ScanBMA.Rd
networkBMA/man/ScanBMAcontrol.Rd
networkBMA/man/contabs.Rd
networkBMA/man/contabs.netwBMA.Rd
networkBMA/man/contabs.prelim.Rd
networkBMA/man/dream4.Rd
networkBMA/man/fastBMAcontrol.Rd
networkBMA/man/fastgControl.Rd
networkBMA/man/gControl.Rd
networkBMA/man/iBMAcontrolLM.Rd
networkBMA/man/iterateBMAlm.Rd
networkBMA/man/networkBMA-internal.Rd
networkBMA/man/networkBMA.Rd
networkBMA/man/roc.Rd
networkBMA/man/scores.Rd
networkBMA/man/summary.networkBMA.Rd
networkBMA/man/varord.Rd
networkBMA/man/vignette.Rd
networkBMA/man/writeEdges.Rd
networkBMA/networkBMA.Rproj
networkBMA/src
networkBMA/src/Makevars
networkBMA/src/Makevars.win
networkBMA/src/MurmurHash3.cpp
networkBMA/src/MurmurHash3.h
networkBMA/src/RcppExports.cpp
networkBMA/src/ScanBMA_full.cpp
networkBMA/src/bmaNoMPI.hpp
networkBMA/src/config.h
networkBMA/src/config.h.in
networkBMA/src/data
networkBMA/src/data/PHH.tab
networkBMA/src/data/brem.data.tab
networkBMA/src/data/data.tab
networkBMA/src/data/prob.tab
networkBMA/src/data/referencePairs.tab
networkBMA/src/data/reg.known.tab
networkBMA/src/data/reg.prob.list
networkBMA/src/data/reg.prob.tab
networkBMA/src/data/timeSeries.tab
networkBMA/src/fastBMA.hpp
networkBMA/src/fastBMAR.cpp
networkBMA/src/include
networkBMA/src/include/cblas.h
networkBMA/src/include/lapacke.h
networkBMA/src/include/lapacke_config.h
networkBMA/src/include/lapacke_mangling.h
networkBMA/src/include/lapacke_utils.h
networkBMA/src/include/old_cblas.h
networkBMA/src/include/old_f77blas.h
networkBMA/src/include/old_lapacke.h
networkBMA/src/include/openblas_config.h
networkBMA/src/lib
networkBMA/src/lib/cmake
networkBMA/src/lib/cmake/openblas
networkBMA/src/my_sort.hpp
networkBMA/src/tclap-1.2.1
networkBMA/src/tclap-1.2.1/AUTHORS
networkBMA/src/tclap-1.2.1/COPYING
networkBMA/src/tclap-1.2.1/ChangeLog
networkBMA/src/tclap-1.2.1/INSTALL
networkBMA/src/tclap-1.2.1/Makefile.am
networkBMA/src/tclap-1.2.1/Makefile.in
networkBMA/src/tclap-1.2.1/NEWS
networkBMA/src/tclap-1.2.1/README
networkBMA/src/tclap-1.2.1/aclocal.m4
networkBMA/src/tclap-1.2.1/config
networkBMA/src/tclap-1.2.1/config/Makefile.am
networkBMA/src/tclap-1.2.1/config/Makefile.in
networkBMA/src/tclap-1.2.1/config/ac_cxx_have_long_long.m4
networkBMA/src/tclap-1.2.1/config/ac_cxx_have_sstream.m4
networkBMA/src/tclap-1.2.1/config/ac_cxx_have_strstream.m4
networkBMA/src/tclap-1.2.1/config/ac_cxx_namespaces.m4
networkBMA/src/tclap-1.2.1/config/ac_cxx_warn_effective_cxx.m4
networkBMA/src/tclap-1.2.1/config/bb_enable_doxygen.m4
networkBMA/src/tclap-1.2.1/config/config.h.in
networkBMA/src/tclap-1.2.1/config/depcomp
networkBMA/src/tclap-1.2.1/config/install-sh
networkBMA/src/tclap-1.2.1/config/missing
networkBMA/src/tclap-1.2.1/config/mkinstalldirs
networkBMA/src/tclap-1.2.1/configure
networkBMA/src/tclap-1.2.1/configure.in
networkBMA/src/tclap-1.2.1/docs
networkBMA/src/tclap-1.2.1/docs/Doxyfile.in
networkBMA/src/tclap-1.2.1/docs/Makefile.am
networkBMA/src/tclap-1.2.1/docs/Makefile.in
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networkBMA/src/tclap-1.2.1/tests/test9.out
networkBMA/src/tclap-1.2.1/tests/test9.sh
networkBMA/vignettes
networkBMA/vignettes/algorithm2e.sty
networkBMA/vignettes/networkBMA.Rnw
networkBMA/vignettes/networkBMA.bib
networkBMA/vignettes/prc-update.pdf
networkBMA/vignettes/relsize.sty
networkBMA/vignettes/roc-update.pdf