Package: cfDNAPro
Type: Package
Title: cfDNAPro extracts and Visualises biological features from whole genome sequencing data of cell-free DNA
Version: 1.9.0
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