dnaEPICO - dnaEPICO: Analysis Pipeline for Illumina DNA Methylation Array Data
A modular and reproducible workflow for preprocessing and analysing Illumina DNA methylation array data from the EPICv2, EPIC, and 450K platforms. It supports quality control, probe filtering, cell-type deconvolution, phenotype preparation, CpG-wise generalised linear models with optional term-level omnibus F tests, longitudinal mixed-effects models using 'lmerTest'/'lme4' or 'nlme', optional 'nlme' residual correlation structures, and automated reports. The workflow uses established Bioconductor tools, including 'minfi', 'ENmix', and 'wateRmelon', and runs locally or in high-performance computing environments.
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softwarepreprocessingmethylationarrayqualitycontrolepigeneticsmicroarraystatisticalmethodchiponchip450k-arrayarrayclockdna-array-methylationepicepic-arrayepicv2epicv2-arraygenomicsglm2illuminalmermethylationmethylation-analysismethylation-annotationmethylation-arraysmethylation-microarraysminfistatistical-analysis
5.82 score 2 stars 5 scripts 444 downloadsGSE280465 - EPICv2 Methylation ExperimentHub Data from GEO
Provides ExperimentHub access to a processed DNA methylation resource derived from GEO accession GSE280465. The resource contains adult Illumina Infinium MethylationEPIC version 2 data from 163 samples across four tissue types, represented as a RangedSummarizedExperiment with beta, M, and CN assays, hg38 genomic ranges, and sample phenotype metadata.
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experimentdataexperimenthubgeohomo_sapiens_datamethylationarraydatamicroarraydatatissueaging-clockbioconductordna-methylationepicv2epigeneticsepigenomewideassociationgenomicsgse280465homo-sapiensillumina-epicv2methylation-arrayrangedsummarizedexperimentsummarizedexperimentzenododatapkg
4.18 score 4 scriptsGSE142512 - 450K and EPIC Methylation ExperimentHub Data from GEO
Provides ExperimentHub access to processed DNA methylation resources derived from GEO accession GSE142512. The resources contain Illumina HumanMethylation450 and Infinium MethylationEPIC data represented as RangedSummarizedExperiment objects with beta, M, and CN assays, hg19 genomic ranges, and sample phenotype metadata.
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experimentdataexperimenthubgeohomo_sapiens_datamethylationarraydatamicroarraydatatissue
3.30 score 4 scriptsGENCODEHub - GENCODE AnnotationHub
Provides access through AnnotationHub to genomic annotation resources derived from GENCODE releases. The release 50 collection represents every feature type in the human GRCh38.p14 GTF. Feature-specific GRanges objects retain the imported identifiers and attributes, while a TxDb resource supports gene, transcript, exon, and coding-sequence queries.
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annotationdataannotationhubgenomicsequencehomo_sapienspackagetypesequenceannotationtxdb
2.70 score 4 scripts