cfDNAPro
This package is for version 3.15 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: 3.15
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("cfDNAPro")):
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")| cfDNAPro Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Sequencing, Software, Visualization, WholeGenome |
| Version | 1.2.0 |
| 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 |
See More
| 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_1.2.0.tar.gz |
| Windows Binary | cfDNAPro_1.2.0.zip |
| macOS Binary (x86_64) | cfDNAPro_1.2.0.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 3.15 | Source Archive |