methBlockR/DESCRIPTION at master · trichelab/methBlockR · GitHub

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Package: methBlockR
Title: cook methylation data down to regulatory blocks for distribution & reuse
Version: 0.9.43
Authors@R: person("Tim","Triche",
                  email = "trichelab@gmail.com",
                  role = c("aut","cre"),
                  comment = c(ORCID = "0000-0001-5665-946X"))
Description: Methylation blocks are a convenient abstraction for 'loci where
             DNA methylation changes concordantly by condition or state'.
             Highlighted by Loyfer (Nature, 2023), this adds a mechanism to
             reconcile data between deep (array) & wide (sequencing) assays.
             This also offers a way to leverage plentiful array-based samples
             without losing key advantages of the sequencing-based assays,
             such as readouts of correlated methylation within fragments.
             It is often true that low-coverage sequencing data are better
             matched by block-wise methylation rates than locus-level ratios.
             Lightweight workflows & classes for preprocessing/QC of Illumina
             methylation data, mostly by sesame and conumee2, are provided to
             complement the 'distillation' of data and evaluate its fidelity.
             Some utilities to ease motif analysis are also included.
Depends: R (>= 4.5),
             SingleCellExperiment,
             ComplexHeatmap,
             sesame,
             iSEE
Imports: SummarizedExperiment,
             ReducedExperiment,
             GenomicRanges,
             BiocParallel,
             rtracklayer,
             matrixStats,
             Rsamtools,
             patchwork,
             circlize,
             RSpectra,
             monaLisa,
             ggplot2,
             methods,
             Seqinfo,
             forcats,
             RcppML,
             Matrix,
             impute,
             uwot,
             mixR
Suggests: CytoSimplex,
             CytoMethIC,
             fastTopics,
             naivebayes,
             CNVRanger,
             CNVfilteR,
             conumee2,
             limma
License: MIT
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
URL: https://github.com/trichelab/methBlockR
BugReports: https://github.com/trichelab/methBlockR/issues