Package: cfDNAPro
Type: Package
Title: cfDNAPro extracts and Visualises biological features from whole
        genome sequencing data of cell-free DNA
Version: 1.16.0
biocViews: Visualization, Sequencing, WholeGenome
Authors@R: c(
    person("Haichao","Wang", email="hw538@cam.ac.uk", role =c("aut","cre")),
    person("Hui","Zhao", email="hui.zhao@cruk.cam.ac.uk", role =c("ctb")),
    person("Elkie","Chan", email="elkie.chan@cruk.cam.ac.uk", role =c("ctb")),
    person("Christopher", "Smith", email="christopher.smith@cruk.cam.ac.uk", role = c("ctb")),
    person("Tomer", "Kaplan", email="tomer.kaplan@cruk.cam.ac.uk", role = c("ctb")),
    person("Florian", "Markowetz", email="florian.markowetz@cruk.cam.ac.uk", role = c("ctb")),
    person("Nitzan","Rosenfeld", email="nitzan.rosenfeld@cruk.cam.ac.uk", role =c("ctb")))
Description: 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.
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
Suggests: scales, ggpubr, knitr (>= 1.23), rmarkdown (>= 1.14),
        devtools (>= 2.3.0), BiocStyle, testthat
License: GPL-3
Encoding: UTF-8
RoxygenNote: 7.2.2
VignetteBuilder: knitr
URL: https://github.com/hw538/cfDNAPro
BugRePORTS: https://github.com/hw538/cfDNAPro/issues
BiocType: Software
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libxml2-dev
        libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:11:06 UTC
RemoteUrl: https://github.com/bioc/cfDNAPro
RemoteRef: RELEASE_3_22
RemoteSha: 910ff773c01a196b424b3fc73e9843c307b948e3
NeedsCompilation: no
Packaged: 2025-11-11 15:37:47 UTC; root
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@cam.ac.uk>
Built: R 4.5.2; ; 2025-11-11 15:49:04 UTC; windows
