cfdnakit

This package is for version 3.21 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: 3.21

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 "4.5") 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 PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CopyNumberVariation, Sequencing, Software, WholeGenome

Version 1.6.0

In Bioconductor since BioC 3.18 (R-4.3) (2 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

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_1.6.0.tar.gz

Windows Binary (x86_64) cfdnakit_1.6.0.zip

macOS Binary (x86_64) cfdnakit_1.6.0.tgz

macOS Binary (arm64) cfdnakit_1.6.0.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

Old Source Packages for BioC 3.21 Source Archive