spiky

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see spiky.

Spike-in calibration for cell-free MeDIP

Bioconductor version: 3.14

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], Jordan Veldboom [ctb], Lauren Harmon [aut], Tim Triche [aut, cre]

Maintainer: Tim Triche <trichelab at gmail.com>

Citation (from within R, enter citation("spiky")):

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("spiky")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("spiky")

Spiky: Analysing cfMeDIP-seq data with spike-in controls	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software
Version	1.0.0
In Bioconductor since	BioC 3.14 (R-4.1) (2.5 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
System Requirements
URL	https://github.com/trichelab/spiky
Bug Reports	https://github.com/trichelab/spiky/issues

Suggests	covr, testthat, equatiomatic, universalmotif, kebabs, ComplexHeatmap, rmarkdown, markdown, knitr, devtools, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg38.masked, BiocManager
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	spiky_1.0.0.tar.gz
Windows Binary	spiky_1.0.0.zip
macOS 10.13 (High Sierra)	spiky_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/spiky
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/spiky
Bioc Package Browser	https://code.bioconductor.org/browse/spiky/
Package Short Url	https://bioconductor.org/packages/spiky/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive