{ "_id": "6a17e777acfb0bcc41da18df", "Package": "cfTools", "Type": "Package", "Title": "Informatics Tools for Cell-Free DNA Study", "Version": "1.13.0", "Authors@R": "c(\nperson(given = \"Ran\",\nfamily = \"Hu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"huran@ucla.edu\",\ncomment = c(ORCID = \"0000-0002-0563-8957\")),\nperson(c(\"Mary\", \"Louisa\"), \"Stackpole\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-4432-6718\")),\nperson(\"Shuo\", \"Li\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-1960-6016\")),\nperson(c(\"Xianghong\", \"Jasmine\"), \"Zhou\",\nrole = \"aut\",\nemail = \"XJZhou@mednet.ucla.edu\",\ncomment = c(ORCID = \"0000-0002-4522-7490\")),\nperson(\"Wenyuan\", \"Li\",\nrole = \"aut\",\nemail = \"WenyuanLi@mednet.ucla.edu\",\ncomment = c(ORCID = \"0000-0002-5029-8525\")))", "Description": "The cfTools R package provides methods for cell-free DNA\n(cfDNA) methylation data analysis to facilitate cfDNA-based\nstudies. Given the methylation sequencing data of a cfDNA\nsample, for each cancer marker or tissue marker, we deconvolve\nthe tumor-derived or tissue-specific reads from all reads\nfalling in the marker region. Our read-based deconvolution\nalgorithm exploits the pervasiveness of DNA methylation for\nsignal enhancement, therefore can sensitively identify a trace\namount of tumor-specific or tissue-specific cfDNA in plasma.\ncfTools provides functions for (1) cancer detection:\nsensitively detect tumor-derived cfDNA and estimate the\ntumor-derived cfDNA fraction (tumor burden); (2) tissue\ndeconvolution: infer the tissue type composition and the cfDNA\nfraction of multiple tissue types for a plasma cfDNA sample.\nThese functions can serve as foundations for more advanced\ncfDNA-based studies, including cancer diagnosis and disease\nmonitoring.", "License": "file LICENSE", "Encoding": "UTF-8", "Config/testthat/edition": "3", "RoxygenNote": "7.2.3", "StagedInstall": "no", "biocViews": "Software, BiomedicalInformatics, Epigenetics, Sequencing,\nMethylSeq, DNAMethylation, DifferentialMethylation", "VignetteBuilder": "knitr", "URL": "https://github.com/jasminezhoulab/cfTools", "BugReports": 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