README.md

In cfDNAPro: This Package Helps Characterise and Visualise Whole Genome Sequencing Data from Liquid Biopsy

cfDNAPro

Liquid Biopsy Cell-free DNA Fragment Size Profiler

cfDNAPro could parse bams files and extract the insert size data. Besides, it also accepts as input the insert sizes metrics files (i.e. txt files ) from picard tools: CollectInsertSizeMetrics.

Introduction

cfDNA fragment size metrics are important features for utilizing liquid biopsy in tumor early detection, diagnosis, therapeutic decision 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.

Installation

For development version:

if (!require(devtools)) install.packages("devtools")
library(devtools)
devtools::install_github("hw538/cfDNAPro", build_vignettes = TRUE)

The steady release has been submitted to Bioconductor, to install:

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

BiocManager::install("cfDNAPro")

Vignettes

To see the vignettes in Rstudio (you have to indicate build_vignettes = TRUE during aforementioned installation step), use the command:

browseVignettes("cfDNAPro")

Citation

Please cite package ‘cfDNAPro’ in publications:

Haichao Wang, Christopher G. Smith, Hui Zhao(2020). cfDNAPro: Liquid Biopsy Cell-free DNA Fragment Size Profiler. R package version 1.1.0 https://github.com/hw538/cfDNAPro

cfDNAPro documentation built on Nov. 8, 2020, 6:49 p.m.