Package: cfdnakit
Title: Fragmen-length analysis package from high-throughput sequencing
        of cell-free DNA (cfDNA)
Version: 1.8.0
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
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: RELEASE_3_22
git_last_commit: 7eac6e7
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 03:05:03 UTC; biocbuild
Author: Pitithat Puranachot [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-6786-9240>)
Maintainer: Pitithat Puranachot <pitithat@gmail.com>
Built: R 4.5.1; ; 2025-10-30 12:08:15 UTC; unix
