cfDNAPro

This is the development version of cfDNAPro; for the stable release version, see cfDNAPro.

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


Bioconductor version: Development (3.20)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Sequencing, Software, Visualization, WholeGenome
Version 1.11.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 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), BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.NCBI.GRCh38
System Requirements
URL https://github.com/hw538/cfDNAPro
See More
Suggests scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package cfDNAPro_1.11.0.tar.gz
Windows Binary cfDNAPro_1.11.0.zip
macOS Binary (x86_64) cfDNAPro_1.11.0.tgz
macOS Binary (arm64) cfDNAPro_1.11.0.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