cfDNAPro

DOI: 10.18129/B9.bioc.cfDNAPro  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see cfDNAPro.

cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA

Bioconductor version: 3.16

cfDNA fragments carry important features for building cancer sample classification ML models, such as fragment size, and fragment end motif etc. Analyzing and visualizing fragment size metrics, as well as other biological features in a curated, standardized, scalable, well-documented, and reproducible way might be time intensive. This package intends to resolve these problems and simplify the process. It offers two sets of functions for cfDNA feature characterization and visualization.

Author: Haichao Wang [aut, cre], Hui Zhao [ctb], Elkie Chan [ctb], Christopher Smith [ctb], Tomer Kaplan [ctb], Florian Markowetz [ctb], Nitzan Rosenfeld [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	1.4.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
License	GPL-3
Depends	R (>= 4.1.0), magrittr (>= 1.5.0)
Imports	tibble, GenomicAlignments, IRanges, plyranges, GenomeInfoDb, GenomicRanges, BiocGenerics, 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	BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, 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_1.4.0.tar.gz
Windows Binary	cfDNAPro_1.4.0.zip
macOS Binary (x86_64)	cfDNAPro_1.4.0.tgz
macOS Binary (arm64)	cfDNAPro_1.4.0.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