{ "_id": "6a3ae1965cdecea1d67efdfa", "Package": "deepSNV", "Maintainer": "Moritz Gerstung ", "License": "GPL-3", "Title": "Detection of subclonal SNVs in deep sequencing data.", "biocViews": "GeneticVariability, SNP, Sequencing, Genetics, DataImport", "Type": "Package", "LazyLoad": "yes", "Authors@R": "c( person(\"Niko\",\"Beerenwinkel\", role=\"ths\"),\nperson(\"Raul\", \"Alcantara\", role=\"ctb\"),\nperson(\"David\", \"Jones\", role = \"ctb\"),\nperson(\"John\", \"Marshall\", role = \"ctb\"),\nperson(\"Inigo\", \"Martincorena\", role = \"ctb\"),\nperson(\"Moritz\",\"Gerstung\",\nemail = \"moritz.gerstung@ebi.ac.uk\", role= c(\"aut\",\"cre\")) )", "Description": "This package provides provides quantitative variant\ncallers for detecting subclonal mutations in ultra-deep (>=100x\ncoverage) sequencing experiments. The deepSNV algorithm is used\nfor a comparative setup with a control experiment of the same\nloci and uses a beta-binomial model and a likelihood ratio test\nto discriminate sequencing errors and subclonal SNVs. The\nshearwater algorithm computes a Bayes classifier based on a\nbeta-binomial model for variant calling with multiple samples\nfor precisely estimating model parameters - such as local error\nrates and dispersion - and prior knowledge, e.g. from variation\ndata bases such as COSMIC.", "Version": "1.59.0", "VignetteBuilder": "knitr", "SystemRequirements": "GNU make", "RoxygenNote": "7.0.2", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:36:15 UTC", "RemoteUrl": "https://github.com/bioc/deepSNV", "RemoteRef": "HEAD", "RemoteSha": "f250bac75e43026adb479ae141b28b3abf296989", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-23 19:22:47 UTC", "User": "root" }, "Author": "Niko Beerenwinkel [ths],\nRaul Alcantara [ctb],\nDavid Jones [ctb],\nJohn Marshall [ctb],\nInigo Martincorena [ctb],\nMoritz Gerstung [aut, cre]", "MD5sum": 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