Files in gevaertlab/EpiMix

EpiMix: an integrative tool for the population-level analysis of DNA methylation

NEWS.md R/ComBat_NoFiles.R R/CpGClustering.R R/EpiMix.R R/EpiMix_helper.R R/GEO_Download_Preprocess.R R/GetNearbyGenes.R R/MethylMix.R R/PlotGene.R R/PlotProbe.R R/Survival.R R/TCGA_Download_Preprocess.R R/TCGA_single_command.R R/correlate_gene_expression.R R/miRNANetwork.R R/util.R README.md inst/unitTests/test_enhancer_mode.R inst/unitTests/test_lncRNA_mode.R inst/unitTests/test_miRNA_mode.R inst/unitTests/test_regular_mode.R longtests/test_GEO_download.R longtests/test_TCGA_getData.R man/BatchCorrection_Combat.Rd man/BatchCorrection_Seurat.Rd man/ClusterProbes.Rd man/ComBat_NoFiles.Rd man/CorrectBatchEffect.Rd man/EpiMix.Rd man/EpiMix_PlotGene.Rd man/EpiMix_PlotModel.Rd man/EpiMix_PlotProbe.Rd man/EpiMix_PlotSurvival.Rd man/EpiMix_getInfiniumAnnotation.Rd man/GEO_Download_DNAMethylation.Rd man/GEO_Download_GeneExpression.Rd man/GEO_EstimateMissingValues_Methylation.Rd man/GEO_EstimateMissingValues_Molecular.Rd man/GEO_GetSampleInfo.Rd man/GEO_getSampleMap.Rd man/Get.Pvalue.p.Rd man/GetNearGenes.Rd man/GetSurvivalProbe.Rd man/MethylMix_MixtureModel.Rd man/MethylMix_ModelSingleGene.Rd man/MethylMix_Predict.Rd man/MethylMix_RemoveFlipOver.Rd man/Preprocess_CancerSite_Methylation27k.Rd man/Preprocess_DNAMethylation.Rd man/Preprocess_GeneExpression.Rd man/Preprocess_MAdata_Cancer.Rd man/Preprocess_MAdata_Normal.Rd man/TCGA_Download_DNAmethylation.Rd man/TCGA_Download_GeneExpression.Rd man/TCGA_EstimateMissingValues_MolecularData.Rd man/TCGA_GENERIC_CheckBatchEffect.Rd man/TCGA_GENERIC_CleanUpSampleNames.Rd man/TCGA_GENERIC_GetSampleGroups.Rd man/TCGA_GENERIC_LoadIlluminaMethylationData.Rd man/TCGA_GENERIC_MET_ClusterProbes_Helper_ClusterGenes_with_hclust.Rd man/TCGA_GENERIC_MergeData.Rd man/TCGA_GetData.Rd man/TCGA_GetSampleInfo.Rd man/TCGA_Load_MethylationData.Rd man/TCGA_Load_MolecularData.Rd man/TCGA_Preprocess_DNAmethylation.Rd man/TCGA_Preprocess_GeneExpression.Rd man/TCGA_Process_EstimateMissingValues.Rd man/TCGA_Select_Dataset.Rd man/addDistNearestTSS.Rd man/addGeneNames.Rd man/betaEst_2.Rd man/blc_2.Rd man/calcDistNearestTSS.Rd man/combineForEachOutput.Rd man/convertAnnotToDF.Rd man/convertGeneNames.Rd man/dot-extractPriMiRNA.Rd man/dot-getComp.Rd man/dot-getMetGroup.Rd man/dot-mapProbeGene.Rd man/dot-splitMetData.Rd man/filterLinearProbes.Rd man/filterMethMatrix.Rd man/filterProbes.Rd man/find_miRNA_targets.Rd man/functionEnrich.Rd man/generateFunctionalPairs.Rd man/get.chromosome.Rd man/get.prevalence.Rd man/getFeatureProbe.Rd man/getFunctionalGenes.Rd man/getLncRNAData.Rd man/getMethStates.Rd man/getMethStates_Helper.Rd man/getProbeAnnotation.Rd man/getRandomGenes.Rd man/getRegionNearGenes.Rd man/getRoadMapEnhancerProbes.Rd man/getTSS.Rd man/get_firehoseData.Rd man/mapTranscriptToGene.Rd man/predictOneGene.Rd man/removeDuplicatedGenes.Rd man/splitmatrix.Rd man/test_gene_expr.Rd man/translateMethylMixResults.Rd man/validEpigenomes.Rd tests/runTests.R vignettes/Methylation_Modeling.Rmd