{ "_id": "6a1e86cd1d7bb097a0a67784", "Package": "chipPCR", "Type": "Package", "Title": "Toolkit of Helper Functions to Pre-Process Amplification Data", "Version": "1.0", "LazyData": "true", "Date": "2021-02-26", "Authors@R": "c(\nperson(\"Stefan\", \"Roediger\",\nemail = \"stefan.roediger@b-tu.de\",\ncomment = c(ORCID = \"0000-0002-1441-6512\"),\nrole = c(\"cre\", \"aut\")),\nperson(\"Michal\", \"Burdukiewicz\",\nemail = \"michalburdukiewicz@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8926-582X\"),\nrole = \"aut\"),\nperson(\"Konstantin A.\", \"Blagodatskikh\",\nemail = \"k.blag@yandex.ru\", role = \"ctb\"),\nperson(\"Andrej-Nikolai\", \"Spiess\",\nemail = \"a.spiess@uke.de\",\nrole = c(\"ctb\"),\ncomment = c(ORCID = \"0000-0002-9630-4724\")))", "Description": "A collection of functions to pre-process amplification\ncurve data from polymerase chain reaction (PCR) or isothermal\namplification reactions. Contains functions to normalize and\nbaseline amplification curves, to detect both the start and end\nof an amplification reaction, several smoothers (e.g., LOWESS,\nmoving average, cubic splines, Savitzky-Golay), a function to\ndetect false positive amplification reactions and a function to\ndetermine the amplification efficiency. Quantification point\n(Cq) methods include the first (FDM) and second approximate\nderivative maximum (SDM) methods (calculated by a\n5-point-stencil) and the cycle threshold method. Data sets of\nexperimental nucleic acid amplification systems ('VideoScan\nHCU', capillary convective PCR (ccPCR)) and commercial systems\nare included. Amplification curves were generated by helicase\ndependent amplification (HDA), ccPCR or PCR. As detection\nsystem intercalating dyes (EvaGreen, SYBR Green) and hydrolysis\nprobes (TaqMan) were used. For more information see: Roediger\net al. 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