CoGAPS: Coordinated Gene Activity in Pattern Sets

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Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.

Author
Elana J. Fertig, Michael F. Ochs
Date of publication
None
Maintainer
Elana J. Fertig <ejfertig@jhmi.edu>
License
GPL (==2)
Version
2.8.0

View on Bioconductor

Man pages

binaryA
'binaryA' creates a binarized heatmap of the A matrix in...
calcCoGAPSStat
'calcCoGAPSStat' calculates the gene set statistics for each...
calcGeneGSStat
'calcGeneGSStat' calculates the probability that a gene...
calcZ
'calcZ' calculates the Z-score for each element based on...
CoGAPS
'CoGAPS' calls the C++ MCMC code through gapsRun and performs...
CoGAPS-package
CoGAPS: Coordinated Gene Activity in Pattern Sets
computeGeneGSProb
CoGAPS gene membership statistic
gapsMapRun
'gapsMapRun' calls the C++ MCMC code and performs Bayesian...
gapsMapTestRun
'gapsMapTestRun' calls the C++ MCMC code and performs...
gapsRun
'gapsRun' calls the C++ MCMC code and performs Bayesian...
gapsTestRun
'gapsTestRun' calls the C++ MCMC code and performs Bayesian...
GIST.D
Sample GIST gene expression data from Ochs et al. (2009).
GIST.S
Sample GIST gene expression data from Ochs et al. (2009).
GSets
Simulated dataset to quantify gene set membership.
plotAtoms
'plotAtoms' a simple plot of the number of atoms from one of...
plotDiag
'plotDiag' plots a series of diagnostic plots
plotGAPS
'plotGAPS' plots the output A and P matrices as a heatmap and...
plotP
'plotP' plots the P matrix in a line plot with error bars
plotSmoothPatterns
'plotSmoothPatterns' plots the output A and P matrices as a...
reorderByPatternMatch
'reorderByPatternMatch' plots the output A and P matrices as...
residuals
'residuals' calculate residuals and produce heatmap
SimpSim.A
Simulated data
SimpSim.D
Simulated data
SimpSim.P
Simulated data
SimpSim.S
Simulated data
tf2ugFC
Gene sets defined by transcription factors defined from...

Files in this package

CoGAPS/COPYING
CoGAPS/DESCRIPTION
CoGAPS/NAMESPACE
CoGAPS/NEWS
CoGAPS/R
CoGAPS/R/CoGAPS.R
CoGAPS/R/RcppExports.R
CoGAPS/R/binaryA.R
CoGAPS/R/calcCoGAPSStat.R
CoGAPS/R/calcGeneGSStat.R
CoGAPS/R/calcZ.R
CoGAPS/R/gapsInterPattern.R
CoGAPS/R/gapsIntraPattern.R
CoGAPS/R/gapsMapRun.R
CoGAPS/R/gapsMapTestRun.R
CoGAPS/R/gapsRun.R
CoGAPS/R/gapsTestRun.R
CoGAPS/R/package.R
CoGAPS/R/plotAtoms.R
CoGAPS/R/plotDiag.R
CoGAPS/R/plotGAPS.R
CoGAPS/R/plotP.R
CoGAPS/R/plotSmoothPatterns.R
CoGAPS/R/reorderByPatternMatch.R
CoGAPS/R/residuals.R
CoGAPS/README.md
CoGAPS/build
CoGAPS/build/vignette.rds
CoGAPS/data
CoGAPS/data/GIST_TS_20084.RData
CoGAPS/data/SimpSim.RData
CoGAPS/data/TFGSList.RData
CoGAPS/inst
CoGAPS/inst/CITATION
CoGAPS/inst/doc
CoGAPS/inst/doc/CoGAPSUsersManual.R
CoGAPS/inst/doc/CoGAPSUsersManual.Rnw
CoGAPS/inst/doc/CoGAPSUsersManual.pdf
CoGAPS/inst/scripts
CoGAPS/inst/scripts/logistic-growth.R
CoGAPS/man
CoGAPS/man/CoGAPS-package.Rd
CoGAPS/man/CoGAPS.Rd
CoGAPS/man/GIST.D.Rd
CoGAPS/man/GIST.S.Rd
CoGAPS/man/GSets.Rd
CoGAPS/man/SimpSim.A.Rd
CoGAPS/man/SimpSim.D.Rd
CoGAPS/man/SimpSim.P.Rd
CoGAPS/man/SimpSim.S.Rd
CoGAPS/man/binaryA.Rd
CoGAPS/man/calcCoGAPSStat.Rd
CoGAPS/man/calcGeneGSStat.Rd
CoGAPS/man/calcZ.Rd
CoGAPS/man/computeGeneGSProb.Rd
CoGAPS/man/gapsMapRun.Rd
CoGAPS/man/gapsMapTestRun.Rd
CoGAPS/man/gapsRun.Rd
CoGAPS/man/gapsTestRun.Rd
CoGAPS/man/plotAtoms.Rd
CoGAPS/man/plotDiag.Rd
CoGAPS/man/plotGAPS.Rd
CoGAPS/man/plotP.Rd
CoGAPS/man/plotSmoothPatterns.Rd
CoGAPS/man/reorderByPatternMatch.Rd
CoGAPS/man/residuals.Rd
CoGAPS/man/tf2ugFC.Rd
CoGAPS/src
CoGAPS/src/AtomicSupport.cc
CoGAPS/src/AtomicSupport.h
CoGAPS/src/GAPSNorm.cpp
CoGAPS/src/GAPSNorm.h
CoGAPS/src/GibbsSampler-atomic.cpp
CoGAPS/src/GibbsSampler-init.cpp
CoGAPS/src/GibbsSampler-update.cpp
CoGAPS/src/GibbsSampler-util.cpp
CoGAPS/src/GibbsSampler.h
CoGAPS/src/GibbsSamplerMap.cpp
CoGAPS/src/GibbsSamplerMap.h
CoGAPS/src/Matrix.cpp
CoGAPS/src/Matrix.h
CoGAPS/src/RcppExports.cpp
CoGAPS/src/cogapsR.cpp
CoGAPS/src/cogapsmapR.cpp
CoGAPS/src/cogapsmaptestR.cpp
CoGAPS/src/cogapstestR.cpp
CoGAPS/src/randgen.cpp
CoGAPS/src/randgen.h
CoGAPS/src/sub_func.cpp
CoGAPS/src/sub_func.h
CoGAPS/tests
CoGAPS/tests/testthat
CoGAPS/tests/testthat.R
CoGAPS/tests/testthat/test_aesthetic.R
CoGAPS/tests/testthat/test_gaps.R
CoGAPS/tests/testthat/test_seed.R
CoGAPS/vignettes
CoGAPS/vignettes/AppNote.bib
CoGAPS/vignettes/CoGAPSUsersManual.Rnw
CoGAPS/vignettes/GISTFigs-Amplitude.pdf
CoGAPS/vignettes/GISTFigs-Patterns.pdf
CoGAPS/vignettes/chicago.sty