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'
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:06:32 UTC
RemoteUrl: https://github.com/bioc/fRagmentomics
RemoteRef: RELEASE_3_23
RemoteSha: bddcbc6d8d71710394a346e021c51e74e7c2905a
NeedsCompilation: no
Packaged: 2026-04-29 21:23:15 UTC; root
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)
Built: R 4.6.0; ; 2026-04-29 21:31:23 UTC; windows
