Package: EpiMix 1.15.0

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]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
EpiMix/json (API)

# Install 'EpiMix' in R:

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

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

On BioConductor:EpiMix-1.15.0(bioc 3.24)EpiMix-1.14.0(bioc 3.23)

software epigenetics preprocessing dnamethylation geneexpression differentialmethylation

4.95 score 2 stars 1 packages 7 scripts 20 exports 121 dependencies

Last updated from:11cb6d5ef9. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	361
linux-devel-x86_64	NOTE	624
source / vignettes	OK	683
linux-release-x86_64	NOTE	688
macos-release-arm64	NOTE	360
macos-oldrel-arm64	NOTE	400
windows-devel	NOTE	518
windows-release	NOTE	489
windows-oldrel	NOTE	487
wasm-release	OK	333

Exports:ClusterProbes EpiMix EpiMix_getInfiniumAnnotation EpiMix_PlotGene EpiMix_PlotModel EpiMix_PlotProbe EpiMix_PlotSurvival find_miRNA_targets functionEnrich GEO_Download_DNAMethylation GEO_Download_GeneExpression GetSurvivalProbe Preprocess_DNAMethylation Preprocess_GeneExpression TCGA_Download_DNAmethylation TCGA_Download_GeneExpression TCGA_GetData TCGA_GetSampleInfo TCGA_Preprocess_DNAmethylation TCGA_Preprocess_GeneExpression

Dependencies:abind AnnotationDbi AnnotationHub askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocVersion biomaRt Biostrings bit bit64 bitops blob cachem cigarillo cli cluster codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray digest doParallel doSNOW downloader dplyr ELMER.data EpiMix.data ExperimentHub farver fastmap filelock foreach formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable hms httr httr2 impute IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle limma magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plyr png prettyunits progress purrr R.matlab R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl restfulr Rhtslib rjson rlang RPMM Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs viridisLite withr XML xml2 XVector yaml

EpiMix

Rendered fromMethylation_Modeling.Rmdusingknitr::rmarkdown

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

Help page	Topics
The extractPriMiRNA function	.extractPriMiRNA
Calculate the distance between probe and gene TSS	addDistNearestTSS
The addGeneNames function	addGeneNames
Calculate distance from region to nearest TSS	calcDistNearestTSS
The ClusterProbes function	ClusterProbes
The EpiMix function	EpiMix
The EpiMix_getInfiniumAnnotation function	EpiMix_getInfiniumAnnotation
The EpiMix_PlotGene function	EpiMix_PlotGene
The EpiMix_PlotModel function.	EpiMix_PlotModel
The EpiMix_PlotProbe function	EpiMix_PlotProbe
EpiMix_PlotSurvival function	EpiMix_PlotSurvival
The filterProbes function	filterProbes
The find_miRNA_targets function	find_miRNA_targets
The functionEnrich function	functionEnrich
The generateFunctionalPairs function	generateFunctionalPairs
The GEO_Download_DNAmethylation function	GEO_Download_DNAMethylation
The GEO_Download_GeneExpression function	GEO_Download_GeneExpression
The GEO_GetSampleInfo function	GEO_GetSampleInfo
the GEO_getSampleMap function	GEO_getSampleMap
Calculate empirical Pvalue	Get.Pvalue.p
getFeatureProbe to select probes within promoter regions or distal regions.	getFeatureProbe
The getMethStates_Helper function	getMethStates_Helper
GetNearGenes to collect nearby genes for one locus.	GetNearGenes
The getProbeAnnotation function	getProbeAnnotation
Identifies nearest genes to a region	getRegionNearGenes
The GetSurvivalProbe function	GetSurvivalProbe
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 function	MethylMix_Predict
The predictOneGene function	predictOneGene
The Preprocess_DNAMethylation function	Preprocess_DNAMethylation
The Preprocess_GeneExpression function	Preprocess_GeneExpression
The removeDuplicatedGenes function	removeDuplicatedGenes
The TCGA_Download_DNAmethylation function	TCGA_Download_DNAmethylation
The TCGA_Download_GeneExpression function	TCGA_Download_GeneExpression
The TCGA_GetData function	TCGA_GetData
The TCGA_GetSampleInfo function	TCGA_GetSampleInfo
The TCGA_Preprocess_DNAmethylation function	TCGA_Preprocess_DNAmethylation
The TCGA_Preprocess_GeneExpression function	TCGA_Preprocess_GeneExpression
The TCGA_Select_Dataset function	TCGA_Select_Dataset
The translateMethylMixResults function	translateMethylMixResults
The validEpigenomes function	validEpigenomes

Package: EpiMix 1.15.0

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

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