Package: EpiMix
Title: EpiMix: an integrative tool for the population-level analysis of
        DNA methylation
Version: 1.14.0
Description: 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@R: c(
             person("Yuanning", "Zheng", email = c("eric2021@stanford.edu"), role = c("aut", "cre")),
             person("Markus", "Sujansky", email = c("sujansky@bc.edu"), role = c("aut")),
             person("John", "Jun", email = c("johnjun094@gmail.com"), role = c("aut")),
             person("Olivier", "Gevaert", email = c("ogevaert@stanford.edu"), role = c("aut"))
             )
Depends: R (>= 4.2.0), EpiMix.data (>= 1.2.2)
License: GPL-3
Encoding: UTF-8
Imports: AnnotationHub, AnnotationDbi, Biobase, biomaRt, data.table,
        doParallel, doSNOW, downloader, dplyr, ELMER.data,
        ExperimentHub, foreach, Seqinfo, GenomicFeatures,
        GenomicRanges, ggplot2, graphics, grDevices, impute, IRanges,
        limma, methods, parallel, plyr, progress, R.matlab,
        RColorBrewer, RCurl, rlang, RPMM, S4Vectors, stats,
        SummarizedExperiment, tibble, tidyr, utils
Suggests: BiocStyle, clusterProfiler, DT, GEOquery, karyoploteR, knitr,
        org.Hs.eg.db, regioneR, Seurat, survival, survminer,
        TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics,
        multiMiR, miRBaseConverter
biocViews: Software, Epigenetics, Preprocessing, DNAMethylation,
        GeneExpression, DifferentialMethylation
RoxygenNote: 7.2.3
VignetteBuilder: knitr
BugReports: https://github.com/gevaertlab/EpiMix/issues
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 12:58:39 UTC
RemoteUrl: https://github.com/bioc/EpiMix
RemoteRef: RELEASE_3_23
RemoteSha: 5ca43ef82cd8670186810a3568381021d29ed79a
NeedsCompilation: no
Packaged: 2026-04-29 21:12:32 UTC; root
Author: Yuanning Zheng [aut, cre],
  Markus Sujansky [aut],
  John Jun [aut],
  Olivier Gevaert [aut]
Maintainer: Yuanning Zheng <eric2021@stanford.edu>
Built: R 4.6.0; ; 2026-04-29 21:18:57 UTC; windows
