cfdnakit

DOI: 10.18129/B9.bioc.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 (3.19)

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>

Installation

To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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")

 

HTML	R Script	cfdnakit vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, Sequencing, Software, WholeGenome
Version	1.1.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	GPL-3
Depends	R (>= 4.3)
Imports	Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges, magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats, rlang
LinkingTo
Suggests	rmarkdown, knitr, roxygen2, BiocStyle
SystemRequirements
Enhances
URL
BugReports	https://github.com/Pitithat-pu/cfdnakit/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	cfdnakit_1.1.0.tar.gz
Windows Binary	cfdnakit_1.1.0.zip
macOS Binary (x86_64)	cfdnakit_1.1.0.tgz
macOS Binary (arm64)
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