cfDNAPro: Liquid Biopsy Cell-Free DNA Fragment Analyser
Welcome to the documentation for cfDNAPro. Use the menu on the left to
explore more about the tool. Below is a brief overview:
Brief Introduction
cfDNAPro is a bioinformatics R package designed for the curation and analysis
of cfDNA fragment features, which play a crucial role in the early detection of
cancer and ongoing disease monitoring. This package facilitates the extraction
of key biological features from cfDNA Next-Generation Sequencing (NGS) data,
including fragment size, fragment end motif, copy number (CN), and mutations.
Analyzing and visualizing these features typically involves using multiple tools,
which can be time-consuming.
To streamline this process, cfDNAPro provides two primary sets of functions: one for data characterization and another for data visualization.
A Quick Example
cfDNAPro can be installed in R by following these instructions (additional details):
if (!require(devtools)) install.packages("devtools")
library(devtools)
devtools::install_github("hw538/cfDNAPro", build_vignettes = TRUE)
To visualise the fragment size mode of each sample,
cfDNAPro can read pre-existing insert size metrics
files from multiple cohort sub-folders stored in
path/to/main/folder:
library(cfDNAPro)
path <- "path/to/main/folder"
myplot <- callMode(path = path) %>% plotMode()
Currently cfDNAPro is compatible exclusively with insert sizes metrics files produced by Picard Tools, using the CollectInsertSizeMetrics tool, which can be accessed here. Future versions will include additional features.
R Package Vignettes
To access the vignettes in RStudio (you have to indicate
build_vignettes = TRUE during the aforementioned installation step), use
the command:
browseVignettes("cfDNAPro")
Citation
If you use cfDNAPro in any published work, please cite:
Haichao Wang, Paulius D. Mennea et al (2020). cfDNAPro:An R/Bioconductor package to extract and visualise cell-free DNA biological features. R package version 1.7 https://github.com/hw538/cfDNAPro
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