spiky
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see spiky.
Spike-in calibration for cell-free MeDIP
Bioconductor version: 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 (x86_64) | 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 [email protected]: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 |