Package: cfDNAPro
Type: Package
Title: cfDNAPro extracts and Visualises biological features from whole
        genome sequencing data of cell-free DNA
Version: 1.13.0
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
git_url: https://git.bioconductor.org/packages/cfDNAPro
git_branch: devel
git_last_commit: 384ebef
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.21
Date/Publication: 2024-12-01
NeedsCompilation: no
Packaged: 2024-12-01 20:46:28 UTC; biocbuild
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 4.5.0; ; 2024-12-02 11:49:25 UTC; unix
