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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "fRagmentomics" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'fRagmentomics: Extract Fragmentomics Features and Mutational Status'
version: 1.1.0
doi: 10.32614/CRAN.package.fRagmentomics
abstract: 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.
authors:
- family-names: Maudet
  given-names: Killian
  email: killian.maudet@gustaveroussy.fr
  orcid: https://orcid.org/0009-0003-3237-092X
- family-names: Samaniego
  given-names: Juliette
  email: juliette.samaniego@gustaveroussy.fr
  orcid: https://orcid.org/0009-0002-3421-1810
- family-names: Pradat
  given-names: Yoann
  email: yoann.pradat@gustaveroussy.fr
  orcid: https://orcid.org/0000-0002-4647-5779
- family-names: Bernard
  given-names: Elsa
  email: elsa.bernard@gustaveroussy.fr
  orcid: https://orcid.org/0000-0002-2057-7187
repository: https://bioc.r-universe.dev
repository-code: https://github.com/ElsaB-Lab/fRagmentomics
commit: 69857f385283d4d00554d0824eecea2cf6cb5659
url: https://github.com/ElsaB-Lab/fRagmentomics
date-released: '2026-04-28'
contact:
- family-names: Maudet
  given-names: Killian
  email: killian.maudet@gustaveroussy.fr
  orcid: https://orcid.org/0009-0003-3237-092X