Package: fRagmentomics
Title: Extract Fragmentomics Features and Mutational Status
Version: 1.0.0
Authors@R: c(
    person("Killian", "Maudet", email = "killian.maudet@gustaveroussy.fr",
        role = c("aut", "cre"), comment = c(ORCID = "0009-0003-3237-092X")),
    person("Juliette", "Samaniego", email = "juliette.samaniego@gustaveroussy.fr",
	   role = "aut", comment = c(ORCID = "0009-0002-3421-1810")),
    person("Yoann", "Pradat", email = "yoann.pradat@gustaveroussy.fr",
	    role = "aut", comment = c(ORCID = "0000-0002-4647-5779")),
    person("Elsa", "Bernard", email = "elsa.bernard@gustaveroussy.fr",
	   role = "aut", comment = c(ORCID = "0000-0002-2057-7187"))
  )
Description: A user-friendly R package that enables the characterization
    of each cfDNA fragment overlapping one or multiple mutations of interest,
    starting from a sequencing file containing aligned reads (BAM file).
    fRagmentomics supports multiple mutation input formats (e.g., VCF, TSV,
    or string "chr:pos:ref:alt" representation), accommodates one-based and
    zero-based genomic conventions, handles mutation representation ambiguities,
    and accepts any reference file and species in FASTA format. For each cfDNA
    fragment, fRagmentomics outputs its size, its 3' and 5' sequences, and its
    mutational status.
    Optionally, when users set apply_bcftools_norm = TRUE, fRagmentomics invokes
    the external command-line tool bcftools norm to left-align and normalize variants.
    If bcftools is not found on the system PATH while this option is enabled,
    the function errors. The package does not install external software; see the
    INSTALL file for per-OS instructions.
URL: https://github.com/ElsaB-Lab/fRagmentomics
BugReports: https://github.com/ElsaB-Lab/fRagmentomics/issues
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
biocViews: Software, Genetics, VariantDetection, IndelDetection,
        Sequencing, DNASeq, Alignment, MultipleSequenceAlignment
Suggests: ragg, covr, testthat (>= 3.0.0), knitr, rmarkdown (>= 1.14),
        BiocStyle
VignetteBuilder: knitr
Config/testthat/edition: 3
Imports: Biostrings, data.table, dplyr, future, future.apply,
        GenomeInfoDb, GenomicRanges, ggh4x, ggplot2, ggseqlogo,
        IRanges, purrr, RColorBrewer, readr, rlang, Rsamtools (>=
        2.4.0), S4Vectors, VariantAnnotation, scales, stringr, tibble,
        tidyr
SystemRequirements: (optional) bcftools (>= 1.21) for VCF
        left-alignment/normalization via 'bcftools norm'
git_url: https://git.bioconductor.org/packages/fRagmentomics
git_branch: RELEASE_3_23
git_last_commit: bddcbc6
git_last_commit_date: 2026-04-28
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28
NeedsCompilation: no
Packaged: 2026-04-28 22:10:03 UTC; biocbuild
Author: Killian Maudet [aut, cre] (ORCID:
    <https://orcid.org/0009-0003-3237-092X>),
  Juliette Samaniego [aut] (ORCID:
    <https://orcid.org/0009-0002-3421-1810>),
  Yoann Pradat [aut] (ORCID: <https://orcid.org/0000-0002-4647-5779>),
  Elsa Bernard [aut] (ORCID: <https://orcid.org/0000-0002-2057-7187>)
Maintainer: Killian Maudet <killian.maudet@gustaveroussy.fr>
Depends: R (>= 4.1.0)
