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)

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DOI: 10.18129/B9.bioc.cfdnakit

Bioconductor version: Development (3.23)

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] ORCID iD ORCID: 0000-0002-6786-9240

Maintainer: Pitithat Puranachot <pitithat at gmail.com>

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

Installation

To install this package, start R (version "4.6") 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.