CoGAPS: Coordinated Gene Activity in Pattern Sets

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.

AuthorElana J. Fertig, Michael F. Ochs
Date of publicationNone
MaintainerElana J. Fertig <ejfertig@jhmi.edu>
LicenseGPL (==2)
Version2.8.0

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...

Functions

binaryA Man page
calcCoGAPSStat Man page
calcGeneGSStat Man page
calcZ Man page
CoGAPS Man page
CoGAPS-package Man page
computeGeneGSProb Man page
gapsMapRun Man page
gapsMapTestRun Man page
gapsRun Man page
gapsTestRun Man page
geneGSProb Man page
GIST.D Man page
GIST.S Man page
GSets Man page
GSets Man page
plotAtoms Man page
plotDiag Man page
plotGAPS Man page
plotP Man page
plotSmoothPatterns Man page
reorderByPatternMatch Man page
residuals Man page
SimpSim.A Man page
SimpSim.D Man page
SimpSim.P Man page
SimpSim.S Man page
tf2ugFC Man page

Files

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

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