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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>

Citation (from within R, enter citation("cfdnakit")):

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")
cfdnakit vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariation, Sequencing, Software, WholeGenome
Version 1.1.2
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
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_1.1.2.tar.gz
Windows Binary
macOS Binary (x86_64) cfdnakit_1.1.2.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