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 (3.24)
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("cfDNAPro")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | Sequencing, Software, Visualization, WholeGenome |
| Version | 1.19.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 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 |
| 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_1.19.0.tar.gz |
| Windows Binary (x86_64) | cfDNAPro_1.19.0.zip |
| macOS Binary (big-sur-x86_64) | cfDNAPro_1.19.0.tgz |
| macOS Binary (sonoma-arm64) | cfDNAPro_1.19.0.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 |