{ "_id": "6a1ad1851d7bb097a09e23a7", "Package": "fRagmentomics", "Title": "Extract Fragmentomics Features and Mutational Status", "Version": "1.1.0", "Authors@R": "c(\nperson(\"Killian\", \"Maudet\", email = \"killian.maudet@gustaveroussy.fr\",\nrole = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0003-3237-092X\")),\nperson(\"Juliette\", \"Samaniego\", email = \"juliette.samaniego@gustaveroussy.fr\",\nrole = \"aut\", comment = c(ORCID = \"0009-0002-3421-1810\")),\nperson(\"Yoann\", \"Pradat\", email = \"yoann.pradat@gustaveroussy.fr\",\nrole = \"aut\", comment = c(ORCID = \"0000-0002-4647-5779\")),\nperson(\"Elsa\", \"Bernard\", email = \"elsa.bernard@gustaveroussy.fr\",\nrole = \"aut\", comment = c(ORCID = \"0000-0002-2057-7187\"))\n)", "Description": "A user-friendly R package that enables the\ncharacterization of each cfDNA fragment overlapping one or\nmultiple mutations of interest, starting from a sequencing file\ncontaining aligned reads (BAM file). fRagmentomics supports\nmultiple mutation input formats (e.g., VCF, TSV, or string\n\"chr:pos:ref:alt\" representation), accommodates one-based and\nzero-based genomic conventions, handles mutation representation\nambiguities, and accepts any reference file and species in\nFASTA format. For each cfDNA fragment, fRagmentomics outputs\nits size, its 3' and 5' sequences, and its mutational status.\nOptionally, when users set apply_bcftools_norm = TRUE,\nfRagmentomics invokes the external command-line tool bcftools\nnorm to left-align and normalize variants. If bcftools is not\nfound on the system PATH while this option is enabled, the\nfunction errors. 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