Files in CoGAPS/CoGAPS

Coordinated Gene Activity in Pattern Sets

.Rbuildignore

.gitattributes

.github/workflows/r-build-check.yml

.gitignore

.travis.yml

ChangeLog

DESCRIPTION

LICENSE

NAMESPACE

NEWS

R/CoGAPS.R R/DistributedCogaps.R R/HelperFunctions.R R/Package.R R/RcppExports.R R/SubsetData.R R/class-CogapsParams.R R/class-CogapsResult.R R/data.R R/methods-CogapsParams.R R/methods-CogapsResult.R README.md

cleanup

configure

configure.ac

configure.win

data/GIST.RData

data/modsimdata.rda

data/modsimresult.rda

inst/CITATION

inst/extdata/GIST.csv

inst/extdata/GIST.gct

inst/extdata/GIST.mtx

inst/extdata/GIST.tsv

inst/extdata/retina_subset_1.h5

inst/extdata/retina_subset_2.h5

inst/extdata/retina_subset_3.h5

inst/extdata/retina_subset_4.h5

inst/scripts/debugRuns.R man/CoGAPS-package.Rd man/CoGAPS.Rd man/CogapsParams-class.Rd man/CogapsParams.Rd man/CogapsResult-class.Rd man/GIST.data_frame.Rd man/GIST.matrix.Rd man/GIST.result.Rd man/GIST.uncertainty.Rd man/GWCoGAPS.Rd man/MANOVA-methods.Rd man/binaryA-methods.Rd man/buildReport.Rd man/calcCoGAPSStat-methods.Rd man/calcGeneGSStat-methods.Rd man/calcZ-methods.Rd man/callInternalCoGAPS.Rd man/checkDataMatrix.Rd man/checkInputs.Rd man/checkpointsEnabled.Rd man/compiledWithOpenMPSupport.Rd man/computeGeneGSProb-methods.Rd man/convertDataToMatrix.Rd man/corcut.Rd man/corrToMeanPattern.Rd man/createCogapsResult.Rd man/createSets.Rd man/distributedCogaps.Rd man/findConsensusMatrix.Rd man/fromCSV-methods.Rd man/gapsCat.Rd man/getAmplitudeMatrix-methods.Rd man/getClusteredPatterns-methods.Rd man/getCorrelationToMeanPattern-methods.Rd man/getDimNames.Rd man/getFeatureLoadings-methods.Rd man/getGeneNames.Rd man/getMeanChiSq-methods.Rd man/getOriginalParameters-methods.Rd man/getParam-methods.Rd man/getPatternGeneSet-methods.Rd man/getPatternMatrix-methods.Rd man/getRetinaSubset.Rd man/getSampleFactors-methods.Rd man/getSampleNames.Rd man/getSubsets-methods.Rd man/getUnmatchedPatterns-methods.Rd man/getValueOrRds.Rd man/getVersion-methods.Rd man/initialize-CogapsParams-method.Rd man/initialize-CogapsResult-method.Rd man/isRdsFile.Rd man/modsimdata.Rd man/modsimresult.Rd man/ncolHelper.Rd man/nrowHelper.Rd man/parseExtraParams.Rd man/patternMarkers-methods.Rd man/patternMatch.Rd man/plotPatternGeneSet-methods.Rd man/plotPatternMarkers-methods.Rd man/plotResiduals-methods.Rd man/reconstructGene-methods.Rd man/sampleUniformly.Rd man/sampleWithAnnotationWeights.Rd man/sampleWithExplictSets.Rd man/scCoGAPS.Rd man/setAnnotationWeights-methods.Rd man/setDistributedParams-methods.Rd man/setFixedPatterns-methods.Rd man/setParam-methods.Rd man/startupMessage.Rd man/stitchTogether.Rd man/supported.Rd man/toCSV-methods.Rd

src/Cogaps.cpp

src/GapsParameters.cpp

src/GapsParameters.h

src/GapsResult.cpp

src/GapsResult.h

src/GapsRunner.cpp

src/GapsRunner.h

src/GapsStatistics.cpp

src/GapsStatistics.h

src/Makevars.in

src/Makevars.win

src/RcppExports.cpp

src/atomic/Atom.cpp

src/atomic/Atom.h

src/atomic/AtomicDomain.cpp

src/atomic/AtomicDomain.h

src/atomic/ConcurrentAtom.cpp

src/atomic/ConcurrentAtom.h

src/atomic/ConcurrentAtomicDomain.cpp

src/atomic/ConcurrentAtomicDomain.h

src/atomic/ProposalQueue.cpp

src/atomic/ProposalQueue.h

src/cpp_tests/catch.h

src/cpp_tests/testConcurrentAtomicDomain.cpp

src/cpp_tests/testDenseGibbsSampler.cpp

src/cpp_tests/testFileParsers.cpp

src/cpp_tests/testHashSets.cpp

src/cpp_tests/testHybridMatrix.cpp

src/cpp_tests/testHybridVector.cpp

src/cpp_tests/testMatrix.cpp

src/cpp_tests/testRandom.cpp

src/cpp_tests/testSamplerHighLevel.cpp

src/cpp_tests/testSerialization.cpp

src/cpp_tests/testSparseGibbsSampler.cpp

src/cpp_tests/testSparseIterator.cpp

src/cpp_tests/testSparseMatrix.cpp

src/cpp_tests/testSparseVector.cpp

src/cpp_tests/testVector.cpp

src/data_structures/HashSets.cpp

src/data_structures/HashSets.h

src/data_structures/HybridMatrix.cpp

src/data_structures/HybridMatrix.h

src/data_structures/HybridVector.cpp

src/data_structures/HybridVector.h

src/data_structures/Matrix.cpp

src/data_structures/Matrix.h

src/data_structures/MutableMap.h

src/data_structures/SparseIterator.cpp

src/data_structures/SparseIterator.h

src/data_structures/SparseMatrix.cpp

src/data_structures/SparseMatrix.h

src/data_structures/SparseVector.cpp

src/data_structures/SparseVector.h

src/data_structures/Vector.cpp

src/data_structures/Vector.h

src/file_parser/CharacterDelimitedParser.cpp

src/file_parser/CharacterDelimitedParser.h

src/file_parser/FileParser.cpp

src/file_parser/FileParser.h

src/file_parser/MatrixElement.cpp

src/file_parser/MatrixElement.h

src/file_parser/MtxParser.cpp

src/file_parser/MtxParser.h

src/gibbs_sampler/AlphaParameters.cpp

src/gibbs_sampler/AlphaParameters.h

src/gibbs_sampler/AsynchronousGibbsSampler.h

src/gibbs_sampler/DenseNormalModel.cpp

src/gibbs_sampler/DenseNormalModel.h

src/gibbs_sampler/SingleThreadedGibbsSampler.h

src/gibbs_sampler/SparseNegativeBinomialModel.cpp

src/gibbs_sampler/SparseNegativeBinomialModel.h

src/gibbs_sampler/SparseNormalModel.cpp

src/gibbs_sampler/SparseNormalModel.h

src/math/Math.cpp

src/math/Math.h

src/math/MatrixMath.cpp

src/math/MatrixMath.h

src/math/Random.cpp

src/math/Random.h

src/math/SIMD.h

src/math/VectorMath.cpp

src/math/VectorMath.h

src/test-runner.cpp

src/utils/Archive.h

src/utils/GapsAssert.h

src/utils/GapsPrint.h

src/utils/GlobalConfig.h

tests/testthat.R tests/testthat/test_checkpoints.R tests/testthat/test_cpp.R tests/testthat/test_getPatternGeneSet.R tests/testthat/test_parameters.R tests/testthat/test_patternMarkers.R tests/testthat/test_seed_consistency.R tests/testthat/test_subset_data.R tests/testthat/test_top_level.R vignettes/CoGAPS.Rmd

vignettes/References.bib

CoGAPS/CoGAPS documentation built on May 2, 2024, 5:24 p.m.