Files in CoGAPS
Coordinated Gene Activity in Pattern Sets

cleanup
NEWS
COPYING
configure.ac
DESCRIPTION
README.md
NAMESPACE
configure.win
configure
inst/CITATION
inst/doc/CoGAPS.R inst/doc/CoGAPS.Rmd
inst/doc/CoGAPS.html
inst/extdata/GIST.mtx
inst/extdata/GIST.gct
inst/extdata/GIST.tsv
inst/extdata/GIST.csv
vignettes/CoGAPS.Rmd
vignettes/old_stuff.txt
vignettes/References.bib
R/CoGAPS.R R/class-CogapsResult.R R/SubsetData.R R/methods-CogapsResult.R R/class-CogapsParams.R R/DistributedCogaps.R R/RcppExports.R R/HelperFunctions.R R/methods-CogapsParams.R R/Package.R
src/GapsStatistics.h
src/Makevars.win
src/GapsParameters.h
src/RcppExports.cpp
src/GapsRunner.h
src/GapsResult.h
src/test-runner.cpp
src/GapsParameters.cpp
src/GapsStatistics.cpp
src/Makevars.in
src/GapsRunner.cpp
src/GapsResult.cpp
src/Cogaps.cpp
src/math/Math.h
src/math/VectorMath.h
src/math/VectorMath.cpp
src/math/MatrixMath.h
src/math/MatrixMath.cpp
src/math/Math.cpp
src/math/Random.cpp
src/math/Random.h
src/math/SIMD.h
src/utils/GapsPrint.h
src/utils/GapsAssert.h
src/utils/GlobalConfig.h
src/utils/Archive.h
src/atomic/AtomAllocator.cpp
src/atomic/AtomAllocator.h
src/atomic/AtomicDomain.cpp
src/atomic/ProposalQueue.cpp
src/atomic/AtomicDomain.h
src/atomic/ProposalQueue.h
src/gibbs_sampler/DenseGibbsSampler.h
src/gibbs_sampler/SparseGibbsSampler.h
src/gibbs_sampler/DenseGibbsSampler.cpp
src/gibbs_sampler/GibbsSampler.h
src/gibbs_sampler/SparseGibbsSampler.cpp
src/cpp_tests/testSparseMatrix.cpp
src/cpp_tests/testSparseIterator.cpp
src/cpp_tests/catch.h
src/cpp_tests/testHashSets.cpp
src/cpp_tests/testAtomicDomain.cpp
src/cpp_tests/testSparseGibbsSampler.cpp
src/cpp_tests/testMatrix.cpp
src/cpp_tests/testSparseVector.cpp
src/cpp_tests/testFileParsers.cpp
src/cpp_tests/testHybridMatrix.cpp
src/cpp_tests/testSerialization.cpp
src/cpp_tests/testVector.cpp
src/cpp_tests/testHybridVector.cpp
src/cpp_tests/testRandom.cpp
src/cpp_tests/testDenseGibbsSampler.cpp
src/data_structures/Matrix.cpp
src/data_structures/HashSets.h
src/data_structures/SparseVector.h
src/data_structures/SparseMatrix.cpp
src/data_structures/HashSets.cpp
src/data_structures/SparseIterator.cpp
src/data_structures/Vector.h
src/data_structures/SparseMatrix.h
src/data_structures/HybridMatrix.h
src/data_structures/HybridMatrix.cpp
src/data_structures/SparseIterator.h
src/data_structures/SparseVector.cpp
src/data_structures/Vector.cpp
src/data_structures/HybridVector.h
src/data_structures/Matrix.h
src/data_structures/HybridVector.cpp
src/file_parser/TsvParser.h
src/file_parser/MatrixElement.h
src/file_parser/MtxParser.h
src/file_parser/CsvParser.h
src/file_parser/CsvParser.cpp
src/file_parser/MtxParser.cpp
src/file_parser/FileParser.cpp
src/file_parser/TsvParser.cpp
src/file_parser/GctParser.h
src/file_parser/FileParser.h
src/file_parser/GctParser.cpp
man/getSampleNames.Rd man/ncolHelper.Rd man/initialize-CogapsResult-method.Rd man/scCoGAPS.Rd man/GWCoGAPS.Rd man/getUnmatchedPatterns-methods.Rd man/corcut.Rd man/supported.Rd man/CogapsParams-class.Rd man/gapsCat.Rd man/startupMessage.Rd man/CoGAPS.Rd man/buildReport.Rd man/getClusteredPatterns-methods.Rd man/binaryA-methods.Rd man/computeGeneGSProb-methods.Rd man/calcZ-methods.Rd man/plotResiduals-methods.Rd man/SimpSim.data.Rd man/sampleWithExplictSets.Rd man/corrToMeanPattern.Rd man/patternMatch.Rd man/setDistributedParams-methods.Rd man/stitchTogether.Rd man/getGeneNames.Rd man/initialize-CogapsParams-method.Rd man/calcGeneGSStat-methods.Rd man/distributedCogaps.Rd man/getCorrelationToMeanPattern-methods.Rd man/parseExtraParams.Rd man/GIST.data_frame.Rd man/GIST.uncertainty.Rd man/tf2ugFC.Rd man/getMeanChiSq-methods.Rd man/CogapsResult-class.Rd man/getOriginalParameters-methods.Rd man/CoGAPS-package.Rd man/createSets.Rd man/nrowHelper.Rd man/checkDataMatrix.Rd man/calcCoGAPSStat-methods.Rd man/GIST.result.Rd man/reconstructGene-methods.Rd man/sampleUniformly.Rd man/SimpSim.result.Rd man/patternMarkers-methods.Rd man/getVersion-methods.Rd man/plotPatternMarkers-methods.Rd man/sampleWithAnnotationWeights.Rd man/findConsensusMatrix.Rd man/getSubsets-methods.Rd man/setParam-methods.Rd man/setAnnotationWeights-methods.Rd man/GIST.matrix.Rd man/getParam-methods.Rd
build/vignette.rds
tests/testthat.R tests/testthat/test_checkpoints.R tests/testthat/test_parameters.R tests/testthat/test_subset_data.R tests/testthat/test_top_level.R tests/testthat/test_cpp.R
tests/testthat/test_ar.temp
data/GIST.RData
data/TFGSList.RData
data/SimpSim.RData
CoGAPS documentation built on Jan. 5, 2019, 6:57 p.m.