cfdnakit
This is the development version of cfdnakit; for the stable release version, see cfdnakit.
Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)
Bioconductor version: Development (3.24)
This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES).
Author: Pitithat Puranachot [aut, cre]
Maintainer: Pitithat Puranachot <pitithat at gmail.com>
citation("cfdnakit")):
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("cfdnakit")
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("cfdnakit")| cfdnakit vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Sequencing, Software, WholeGenome |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | GPL-3 |
| Depends | R (>= 4.3) |
| Imports | Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges, magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats, rlang |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/Pitithat-pu/cfdnakit/issues |
See More
| Suggests | rmarkdown, knitr, roxygen2, BiocStyle |
| 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 | cfdnakit_1.11.0.tar.gz |
| Windows Binary (x86_64) | cfdnakit_1.11.0.zip |
| macOS Binary (big-sur-x86_64) | cfdnakit_1.11.0.tgz |
| macOS Binary (sonoma-arm64) | cfdnakit_1.11.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cfdnakit |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cfdnakit |
| Bioc Package Browser | https://code.bioconductor.org/browse/cfdnakit/ |
| Package Short Url | https://bioconductor.org/packages/cfdnakit/ |
| Package Downloads Report | Download Stats |