cfDNAPro

This package is for version 3.14 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: 3.14

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>

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

Installation

To install this package, start R (version "4.1") 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")

cfDNAPro Tutorial HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Sequencing, Software, Visualization, WholeGenome

Version 1.0.0

In Bioconductor since BioC 3.12 (R-4.0) (3.5 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)

System Requirements

URL https://github.com/hw538/cfDNAPro

Suggests scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat

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 cfDNAPro_1.0.0.tar.gz

Windows Binary cfDNAPro_1.0.0.zip

macOS 10.13 (High Sierra) cfDNAPro_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/cfDNAPro

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cfDNAPro

Bioc Package Browser https://code.bioconductor.org/browse/cfDNAPro/

Package Short Url https://bioconductor.org/packages/cfDNAPro/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.14 Source Archive