DOI: 10.18129/B9.bioc.cfDNAPro  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see cfDNAPro.

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

Bioconductor version: 3.16

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>

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biocViews Sequencing, Software, Visualization, WholeGenome
Version 1.4.0
In Bioconductor since BioC 3.12 (R-4.0) (2.5 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)
Suggests BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg19, scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14), devtools (>= 2.3.0), BiocStyle, testthat
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