cfdnakit
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see cfdnakit.
Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)
Bioconductor version: 3.19
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")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.2.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| 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_1.2.0.tar.gz |
| Windows Binary (x86_64) | cfdnakit_1.2.0.zip |
| macOS Binary (x86_64) | cfdnakit_1.2.0.tgz |
| macOS Binary (arm64) | cfdnakit_1.2.0.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 |