DOI: 10.18129/B9.bioc.spiky  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see spiky.

Spike-in calibration for cell-free MeDIP

Bioconductor version: 3.16

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.

Author: Samantha Wilson [aut], Lauren Harmon [aut], Tim Triche [aut, cre]

Maintainer: Tim Triche <trichelab at gmail.com>

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biocViews DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software
Version 1.4.0
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
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, equatiomatic, universalmotif, kebabs, ComplexHeatmap, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager
URL https://github.com/trichelab/spiky
BugReports https://github.com/trichelab/spiky/issues
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