spiky
Spike-in calibration for cell-free MeDIP
Bioconductor version: Release (3.19)
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>
citation("spiky")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software |
Version | 1.10.0 |
In Bioconductor since | BioC 3.14 (R-4.1) (3 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 |
See More
Suggests | covr, testthat, 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_1.10.0.tar.gz |
Windows Binary | spiky_1.10.0.zip |
macOS Binary (x86_64) | spiky_1.10.0.tgz |
macOS Binary (arm64) | spiky_1.10.0.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 3.19 | Source Archive |