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cfdnakit

This is the development version of cfdnakit; to use it, please install the devel version of Bioconductor.

Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA)

Bioconductor version: Development (3.18)

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 "4.3") 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 0.99.4
In Bioconductor since BioC 3.18 (R-4.3)
License GPL-3
Depends R (>= 4.3)
Imports Biobase, dplyr, GenomicRanges, GenomeInfoDb, ggplot2, IRanges, magrittr, PSCBS, QDNAseq, Rsamtools, utils, S4Vectors, stats, rlang
Linking To
Suggests rmarkdown, knitr, roxygen2, BiocStyle
System Requirements
Enhances
URL
Bug Reports https://github.com/Pitithat-pu/cfdnakit/issues
See More
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_0.99.4.tar.gz
Windows Binary cfdnakit_0.99.4.zip
macOS Binary (x86_64) cfdnakit_0.99.4.tgz
macOS Binary (arm64) cfdnakit_0.99.4.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