Package: spiky
Type: Package
Title: Spike-in calibration for cell-free MeDIP
Description: spiky implements methods and model generation for cfMeDIP
        (cell-free methylated DNA immunoprecipitation) with spike-in
        controls. CfMeDIP is an enrichment protocol which avoids
        destructive conversion of scarce template, making it ideal as a
        "liquid biopsy," but creating certain challenges in comparing
        results across specimens, subjects, and experiments. The use of
        synthetic spike-in standard oligos allows diagnostics performed
        with cfMeDIP to quantitatively compare samples across subjects,
        experiments, and time points in both relative and absolute
        terms.
Version: 1.16.0
Date: 2023-04-19
Authors@R: c(person("Samantha", "Wilson", role=c("aut")), 
             person("Lauren", "Harmon", role=c("aut")),
             person("Tim", "Triche", role=c("aut","cre"),
                    email="trichelab@gmail.com"))
biocViews: DifferentialMethylation, DNAMethylation, Normalization,
        Preprocessing, QualityControl, Sequencing
URL: https://github.com/trichelab/spiky
BugReports: https://github.com/trichelab/spiky/issues
License: GPL-2
Depends: Rsamtools, GenomicRanges, R (>= 3.6.0)
Imports: stats, scales, bamlss, methods, tools, IRanges, Biostrings,
        GenomicAlignments, BlandAltmanLeh, GenomeInfoDb, BSgenome,
        S4Vectors, graphics, ggplot2, utils
Suggests: covr, testthat, rmarkdown, markdown, knitr, devtools,
        BSgenome.Mmusculus.UCSC.mm10.masked,
        BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager
RoxygenNote: 7.2.1
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: true
Config/pak/sysreqs: make libbz2-dev liblzma-dev libxml2-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:10:11 UTC
RemoteUrl: https://github.com/bioc/spiky
RemoteRef: RELEASE_3_22
RemoteSha: e4c8b369131e3ea4301228a25c74bd30a3c9923d
NeedsCompilation: no
Packaged: 2026-03-12 08:39:49 UTC; root
Author: Samantha Wilson [aut],
  Lauren Harmon [aut],
  Tim Triche [aut, cre]
Maintainer: Tim Triche <trichelab@gmail.com>
Built: R 4.5.2; ; 2026-03-12 08:44:09 UTC; windows
