Package: EpiMix 1.9.0

Yuanning Zheng

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

EpiMix is a comprehensive tool for the integrative analysis of high-throughput DNA methylation data and gene expression data. EpiMix enables automated data downloading (from TCGA or GEO), preprocessing, methylation modeling, interactive visualization and functional annotation.To identify hypo- or hypermethylated CpG sites across physiological or pathological conditions, EpiMix uses a beta mixture modeling to identify the methylation states of each CpG probe and compares the methylation of the experimental group to the control group.The output from EpiMix is the functional DNA methylation that is predictive of gene expression. EpiMix incorporates specialized algorithms to identify functional DNA methylation at various genetic elements, including proximal cis-regulatory elements of protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs.

Authors:Yuanning Zheng [aut, cre], Markus Sujansky [aut], John Jun [aut], Olivier Gevaert [aut]

EpiMix_1.9.0.tar.gz
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EpiMix_1.9.0.tgz(r-4.4-any)EpiMix_1.9.0.tgz(r-4.3-any)
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EpiMix.pdf |EpiMix.html✨
EpiMix/json (API)

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

Peer review:

Bug tracker:https://github.com/gevaertlab/epimix/issues

On BioConductor:EpiMix-1.9.0(bioc 3.21)EpiMix-1.8.0(bioc 3.20)

softwareepigeneticspreprocessingdnamethylationgeneexpressiondifferentialmethylation

4.65 score 1 stars 1 packages 7 scripts 140 downloads 20 exports 128 dependencies

Last updated 2 months agofrom:0b423e192d. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 27 2024
R-4.5-winNOTENov 27 2024
R-4.5-linuxNOTENov 27 2024
R-4.4-winNOTENov 27 2024
R-4.4-macNOTENov 27 2024
R-4.3-winNOTENov 27 2024
R-4.3-macNOTENov 27 2024

Exports:ClusterProbesEpiMixEpiMix_getInfiniumAnnotationEpiMix_PlotGeneEpiMix_PlotModelEpiMix_PlotProbeEpiMix_PlotSurvivalfind_miRNA_targetsfunctionEnrichGEO_Download_DNAMethylationGEO_Download_GeneExpressionGetSurvivalProbePreprocess_DNAMethylationPreprocess_GeneExpressionTCGA_Download_DNAmethylationTCGA_Download_GeneExpressionTCGA_GetDataTCGA_GetSampleInfoTCGA_Preprocess_DNAmethylationTCGA_Preprocess_GeneExpression

Dependencies:abindAnnotationDbiAnnotationHubaskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbitbit64bitopsblobcachemcliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdoParalleldoSNOWdownloaderdplyrELMER.dataEpiMix.dataExperimentHubfansifarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehmshttrhttr2imputeIRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmamagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR.matlabR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRPMMRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLxml2XVectoryamlzlibbioc

EpiMix

| Yuanning Zheng, John Jun, Kevin Brennan and Olivier Gevaert | | Stanford Center for Biomedical Informatics Research (BIMR) | Department of Medicine | 1265 Welch Road | Stanford CA, 94305-5479

Rendered fromMethylation_Modeling.Rmdusingknitr::rmarkdownon Nov 27 2024.

Last update: 2023-07-11
Started: 2022-06-02

Readme and manuals

Help Manual

Help pageTopics
The extractPriMiRNA function.extractPriMiRNA
Calculate the distance between probe and gene TSSaddDistNearestTSS
The addGeneNames functionaddGeneNames
Calculate distance from region to nearest TSScalcDistNearestTSS
The ClusterProbes functionClusterProbes
The EpiMix functionEpiMix
The EpiMix_getInfiniumAnnotation functionEpiMix_getInfiniumAnnotation
The EpiMix_PlotGene functionEpiMix_PlotGene
The EpiMix_PlotModel function.EpiMix_PlotModel
The EpiMix_PlotProbe functionEpiMix_PlotProbe
EpiMix_PlotSurvival functionEpiMix_PlotSurvival
The filterProbes functionfilterProbes
The find_miRNA_targets functionfind_miRNA_targets
The functionEnrich functionfunctionEnrich
The generateFunctionalPairs functiongenerateFunctionalPairs
The GEO_Download_DNAmethylation functionGEO_Download_DNAMethylation
The GEO_Download_GeneExpression functionGEO_Download_GeneExpression
The GEO_GetSampleInfo functionGEO_GetSampleInfo
the GEO_getSampleMap functionGEO_getSampleMap
Calculate empirical PvalueGet.Pvalue.p
getFeatureProbe to select probes within promoter regions or distal regions.getFeatureProbe
The getMethStates_Helper functiongetMethStates_Helper
GetNearGenes to collect nearby genes for one locus.GetNearGenes
The getProbeAnnotation functiongetProbeAnnotation
Identifies nearest genes to a regiongetRegionNearGenes
The GetSurvivalProbe functionGetSurvivalProbe
getTSS to fetch GENCODE gene annotation (transcripts level) from Bioconductor package biomaRt If upstream and downstream are specified in TSS list, promoter regions of GENCODE gene will be generated.getTSS
The MethylMix_Predict functionMethylMix_Predict
The predictOneGene functionpredictOneGene
The Preprocess_DNAMethylation functionPreprocess_DNAMethylation
The Preprocess_GeneExpression functionPreprocess_GeneExpression
The removeDuplicatedGenes functionremoveDuplicatedGenes
The TCGA_Download_DNAmethylation functionTCGA_Download_DNAmethylation
The TCGA_Download_GeneExpression functionTCGA_Download_GeneExpression
The TCGA_GetData functionTCGA_GetData
The TCGA_GetSampleInfo functionTCGA_GetSampleInfo
The TCGA_Preprocess_DNAmethylation functionTCGA_Preprocess_DNAmethylation
The TCGA_Preprocess_GeneExpression functionTCGA_Preprocess_GeneExpression
The TCGA_Select_Dataset functionTCGA_Select_Dataset
The translateMethylMixResults functiontranslateMethylMixResults
The validEpigenomes functionvalidEpigenomes