Package: cfdnakit
Title: Fragmen-length analysis package from high-throughput sequencing of cell-free DNA (cfDNA) 
Version: 1.9.0
Authors@R: person(given = "Pitithat",
           family = "Puranachot",
           role = c("aut", "cre"),
           email = "pitithat@gmail.com",
           comment = c(ORCID = "0000-0002-6786-9240"))
Description: This package provides basic functions for analyzing shallow whole-genome sequencing (~0.3X or more) of cell-free DNA (cfDNA). The package basically extracts the length of cfDNA fragments and aids the vistualization of fragment-length information. The package also extract fragment-length information per non-overlapping fixed-sized bins and used it for calculating ctDNA estimation score (CES).  
License: GPL-3
Encoding: UTF-8
LazyData: FALSE
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
biocViews: CopyNumberVariation, Sequencing, WholeGenome
BugReports: https://github.com/Pitithat-pu/cfdnakit/issues
Imports: 
    Biobase,
    dplyr,
    GenomicRanges,
    GenomeInfoDb,
    ggplot2,
    IRanges,
    magrittr,
    PSCBS,
    QDNAseq,
    Rsamtools,
    utils,
    S4Vectors,
    stats,
    rlang
Depends: 
    R (>= 4.3)
Suggests: 
    rmarkdown,
    knitr,
    roxygen2,
    BiocStyle
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/cfdnakit
git_branch: devel
git_last_commit: 17e7520
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
