Package: CoGAPS 3.27.0

Elana J. Fertig

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.

Authors:Jeanette Johnson, Ashley Tsang, Jacob Mitchell, Thomas Sherman, Wai-shing Lee, Conor Kelton, Ondrej Maxian, Jacob Carey, Genevieve Stein-O'Brien, Michael Considine, Maggie Wodicka, John Stansfield, Shawn Sivy, Carlo Colantuoni, Alexander Favorov, Mike Ochs, Elana Fertig

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CoGAPS.pdf |CoGAPS.html✨
CoGAPS/json (API)
NEWS

# Install 'CoGAPS' in R:
install.packages('CoGAPS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On BioConductor:CoGAPS-3.27.0(bioc 3.21)CoGAPS-3.26.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpressiontranscriptiongenesetenrichmentdifferentialexpressionbayesianclusteringtimecoursernaseqmicroarraymultiplecomparisondimensionreductionimmunooncologycpp

6.80 score 104 scripts 576 downloads 14 mentions 37 exports 81 dependencies

Last updated 2 months agofrom:ec59da0c3b. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-win-x86_64NOTENov 29 2024
R-4.5-linux-x86_64NOTENov 29 2024
R-4.4-win-x86_64NOTENov 29 2024
R-4.4-mac-x86_64NOTENov 29 2024
R-4.4-mac-aarch64NOTENov 29 2024
R-4.3-win-x86_64NOTENov 29 2024
R-4.3-mac-x86_64NOTENov 29 2024
R-4.3-mac-aarch64NOTENov 29 2024

Exports:binaryAbuildReportcalcCoGAPSStatcalcZcheckpointsEnabledCoGAPSCogapsParamscompiledWithOpenMPSupportfindConsensusMatrixfromCSVgetAmplitudeMatrixgetClusteredPatternsgetCorrelationToMeanPatterngetFeatureLoadingsgetMeanChiSqgetOriginalParametersgetParamgetPatternGeneSetgetPatternMatrixgetRetinaSubsetgetSampleFactorsgetSubsetsgetUnmatchedPatternsgetVersionGWCoGAPSMANOVApatternMarkersplotPatternGeneSetplotPatternMarkersplotResidualsreconstructGenescCoGAPSsetAnnotationWeightssetDistributedParamssetFixedPatternssetParamtoCSV

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelbitopscaToolscliclustercodetoolscolorspacecowplotcpp11crayoncurldata.tableDelayedArraydplyrfansifarverfastmatchfgseaforcatsformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegplotsgtablegtoolshttrIRangesisobandjsonliteKernSmoothlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRcpprhdf5rhdf5filtersRhdf5librlangS4ArraysS4VectorsscalesSingleCellExperimentsnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

CoGAPS - Coordinated Gene Association in Pattern Sets

Jeanette Johnson, Ashley Tsang, Thomas Sherman, Genevieve Stein-O'Brien, Hyejune Limb, Elana Fertig

Rendered fromCoGAPS.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2024-06-17
Started: 2018-08-02

Readme and manuals

Help Manual

Help pageTopics
CoGAPS: Coordinated Gene Activity in Pattern SetsCoGAPS-package
binary heatmap for standardized feature matrixbinaryA binaryA,CogapsResult-method
Information About Package CompilationbuildReport
calculate statistic on sets of measurements (genes) or samplescalcCoGAPSStat calcCoGAPSStat,CogapsResult-method
probability gene belongs in gene setcalcGeneGSStat calcGeneGSStat,CogapsResult-method
compute z-score matrixcalcZ calcZ,CogapsResult-method
Check if package was built with checkpoints enabledcheckpointsEnabled
CoGAPS Matrix Factorization AlgorithmCoGAPS
CogapsParams constructorCogapsParams
CogapsParamsCogapsParams-class
CogapsResultCogapsResult-class
Check if compiler supported OpenMPcompiledWithOpenMPSupport
compute gene probabilitycomputeGeneGSProb computeGeneGSProb,CogapsResult-method
find the consensus pattern matrix across all subsetsfindConsensusMatrix
read CoGAPS Result object from a directory with a set of csvs see toCSVfromCSV fromCSV,character-method
return Amplitude matrix from CogapsResult objectgetAmplitudeMatrix getAmplitudeMatrix,CogapsResult-method
return clustered patterns from set of all patterns across all subsetsgetClusteredPatterns getClusteredPatterns,CogapsResult-method
return correlation between each pattern and the cluster meangetCorrelationToMeanPattern getCorrelationToMeanPattern,CogapsResult-method
return featureLoadings matrix from CogapsResult objectgetFeatureLoadings getFeatureLoadings,CogapsResult-method
return chi-sq of final matricesgetMeanChiSq getMeanChiSq,CogapsResult-method
return original parameters used to generate this resultgetOriginalParameters getOriginalParameters,CogapsResult-method
get the value of a parametergetParam getParam,CogapsParams-method
generate statistics associating patterns with gene setsgetPatternGeneSet getPatternGeneSet,CogapsResult,list,character-method
return pattern matrix from CogapsResult objectgetPatternMatrix getPatternMatrix,CogapsResult-method
get specified number of retina subsetsgetRetinaSubset
return sampleFactors matrix from CogapsResult objectgetSampleFactors getSampleFactors,CogapsResult-method
return the names of the genes (samples) in each subsetgetSubsets getSubsets,CogapsResult-method
return unmatched patterns from each subsetgetUnmatchedPatterns getUnmatchedPatterns,CogapsResult-method
return version number used to generate this resultgetVersion getVersion,CogapsResult-method
GIST gene expression data from Ochs et al. (2009)GIST.data_frame
GIST gene expression data from Ochs et al. (2009)GIST.matrix
CoGAPS result from running on GIST datasetGIST.result
GIST gene expression uncertainty matrix from Ochs et al. (2009)GIST.uncertainty
Genome Wide CoGAPSGWCoGAPS
constructor for CogapsParamsinitialize,CogapsParams-method
Constructor for CogapsResultinitialize,CogapsResult-method
MANOVA statistical test for patterns between sample groupsMANOVA MANOVA,matrix,CogapsResult-method
Toy example to run CoGAPS on.modsimdata
Result of applying CoGAPS on the Toy example.modsimresult
compute pattern markers statisticpatternMarkers patternMarkers,CogapsResult-method
generate a barchart of most significant hallmark sets for a patternplotPatternGeneSet plotPatternGeneSet,list,numeric,numeric-method
heatmap of original data clustered by pattern markers statisticplotPatternMarkers
plot of residualsplotResiduals plotResiduals,CogapsResult-method
reconstruct genereconstructGene reconstructGene,CogapsResult-method
Single Cell CoGAPSscCoGAPS
set the annotation labels and weights for subsetting the datasetAnnotationWeights setAnnotationWeights,CogapsParams-method
set the value of parameters for distributed CoGAPSsetDistributedParams setDistributedParams,CogapsParams-method
set the fixed patterns for either the A or the P matrixsetFixedPatterns setFixedPatterns,CogapsParams-method
set the value of a parametersetParam setParam,CogapsParams-method
save CoGAPS Result object as a set of csvs to directory see fromCSVtoCSV toCSV,CogapsResult,character-method