https://paulyrp.r-universe.devRecent package updates in paulyrpR-universehttps://github.com/paulyrp.pnghttps://paulyrp.r-universe.devMon, 07 Sep 2026 00:23:21 GMTruizpint@qut.edu.au (Paul Ruiz)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.https://github.com/r-universe/biocstaging/actions/runs/37620034320Mon, 07 Sep 2026 00:23:21 GMTGSE1425120.99.2successhttps://biocstaging.r-universe.devhttps://github.com/BiocStaging/GSE142512GSE142512.RmdGSE142512.htmlGSE142512 DNA methylation data2026-07-05 22:01:192026-09-07 00:23:21ruizpint@qut.edu.au (Paul Ruiz Pinto)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.https://github.com/r-universe/bioc/actions/runs/39019479545Tue, 18 Aug 2026 09:14:34 GMTdnaEPICO0.99.38successhttps://bioc.r-universe.devhttps://github.com/bioc/dnaEPICOdnaEPICO-overview.RmddnaEPICO-overview.htmldnaEPICO Overview2026-05-23 10:49:012026-08-11 15:21:32dnaEPICO-local.RmddnaEPICO-local.htmlLocal Use of dnaEPICO2026-04-22 11:07:252026-08-11 15:21:32dnaEPICO-pipeline.RmddnaEPICO-pipeline.htmlPipeline Use of dnaEPICO2026-04-22 11:07:252026-08-18 09:14:34ruizpint@qut.edu.au (Paul Ruiz Pinto)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.https://github.com/r-universe/biocstaging/actions/runs/37617101733Sat, 08 Aug 2026 09:36:37 GMTGENCODEHub0.99.0successhttps://biocstaging.r-universe.devhttps://github.com/BiocStaging/GENCODEHubGENCODEHub.RmdGENCODEHub.htmlGENCODE AnnotationHub2026-08-04 11:05:042026-08-08 09:36:37ruizpint@qut.edu.au (Paul Ruiz)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.https://github.com/r-universe/bioc/actions/runs/38727659212Fri, 07 Aug 2026 01:11:20 GMTGSE2804650.99.1successhttps://bioc.r-universe.devhttps://github.com/bioc/GSE280465GSE280465.RmdGSE280465.htmlGSE280465 EPICv2 methylation data2026-07-05 10:27:172026-07-05 10:27:17