cfDNAPro

DOI: 10.18129/B9.bioc.cfDNAPro    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see cfDNAPro.

cfDNAPro Helps Characterise and Visualise Whole Genome Sequencing Data from Liquid Biopsy

Bioconductor version: 3.15

cfDNA fragment size metrics are important features for utilizing liquid biopsy in tumor early detection, diagnosis, therapy personlization and monitoring. Analyzing and visualizing insert size metrics could be time intensive. This package intends to simplify this exploration process, and it offers two sets of functions for data characterization and data visualization.

Author: Haichao Wang [aut, cre], Nitzan Rosenfeld [ctb], Hui Zhao [ctb], Christopher Smith [ctb]

Maintainer: Haichao Wang <hw538 at cam.ac.uk>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("cfDNAPro")

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("cfDNAPro")

 

HTML	R Script	cfDNAPro Tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	Sequencing, Software, Visualization, WholeGenome
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (2 years)
License	GPL-3
Depends	R (>= 4.0), magrittr (>= 1.5.0)
Imports	stats, utils, dplyr (>= 0.8.3), stringr (>= 1.4.0), quantmod (>= 0.4), ggplot2 (>= 3.2.1), Rsamtools(>= 2.4.0), rlang (>= 0.4.0)
LinkingTo
Suggests	scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat
SystemRequirements
Enhances
URL	https://github.com/hw538/cfDNAPro
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	cfDNAPro_1.2.0.tar.gz
Windows Binary	cfDNAPro_1.2.0.zip
macOS Binary (x86_64)	cfDNAPro_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cfDNAPro
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cfDNAPro
Package Short Url	https://bioconductor.org/packages/cfDNAPro/
Package Downloads Report	Download Stats