spiky
This is the development version of spiky; for the stable release version, see spiky.
Spike-in calibration for cell-free MeDIP
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.19.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (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 |
| 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_1.19.0.tar.gz |
| Windows Binary (x86_64) | spiky_1.19.0.zip |
| macOS Binary (big-sur-x86_64) | spiky_1.19.0.tgz |
| macOS Binary (sonoma-arm64) | spiky_1.19.0.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 |