Files in gevaertlab/EpiMix
EpiMix: an integrative tool for the population-level analysis of DNA methylation
.BBSoptions
.RData
.gitignore
DESCRIPTION
NAMESPACE
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
vignettes/figures/Workflow.png
vignettes/figures/plot_gene.png
vignettes/figures/plot_probe.png
vignettes/style.css
