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It provides copy number adjusted for purity and ploidy and can\nclassify mutations by somatic status and clonality. It requires a pool of\nprocess-matched normals for coverage normalization and artifact filtering.\nPureCN was parameterized using large collections of diverse samples, ranging\nfrom low coverage whole-exome to ultra-deep sequenced plasma gene-panels.\n\n## Installation\n\nTo install this package, start R and enter:\n\n```\nif (!requireNamespace(\"BiocManager\", quietly = TRUE))\n    install.packages(\"BiocManager\")\nBiocManager::install(\"PureCN\")\n```\n\nIf your R/Bioconductor version is\n[outdated](https://bioconductor.org/about/release-announcements/), this will\ninstall an old and unsupported version.\n\nFor outdated R/Bioconductor versions, you can try backporting the latest stable\nversion (this should work fine for Bioconductor 3.3 and later):\n\n```\nBiocManager::install(\"lima1/PureCN\", ref = \"RELEASE_3_21\")\n```\n\nIf you want the latest and greatest from the developer branch:\n\n```\nBiocManager::install(\"lima1/PureCN\")\n```\n\nTo get the lastest stable version from\n[Conda](https://anaconda.org/bioconda/bioconductor-purecn) (unstable is\ncurrently only available from GitHub directly):\n\n```\nconda install -c bioconda bioconductor-purecn=2.12.0\n```\n\nA [Dockerhub](https://hub.docker.com/r/markusriester/purecn) image of the\nlatest stable version with recommended dependencies such as\n[GenomicsDB](https://github.com/GenomicsDB/GenomicsDB) and\n[GATK 4](https://github.com/broadinstitute/gatk) pre-installed:\n\n```\ndocker pull markusriester/purecn:latest\n```\n\n\n## Tutorials\n\nTo get started:\n\n```\nvignette(\"Quick\", package = \"PureCN\")\n```\n\nFor the R package and more detailed information:\n\n```\nvignette(\"PureCN\", package = \"PureCN\")\n```\n\nThese tutorials are also available on the Bioconductor project page\n([devel](https://bioconductor.org/packages/devel/bioc/html/PureCN.html),\n[stable](https://doi.org/doi:10.18129/B9.bioc.PureCN)).\n\n## Bugs\n\nBefore [posting](https://github.com/lima1/PureCN/issues) a bug report:\n\n* update to the latest version \n* confirm with sessionInfo() that the latest version is used\n* if this is a first PureCN attempt, closely follow the Quick vignette \n([devel](https://bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html),\n[stable](https://bioconductor.org/packages/release/bioc/vignettes/PureCN/inst/doc/Quick.html))\n* make sure that the issue is not covered in the Support section of the main\n  vignette\n\n## Papers\n\n* Main paper describing the likelihood model:\n\n    Riester M, Singh A, Brannon A, Yu K, Campbell C, Chiang D and Morrissey M\n    (2016). “PureCN: Copy number calling and SNV classification using targeted\n    short read sequencing.” _Source Code for Biology and Medicine_, **11**, pp. 13.\n    doi: [10.1186/s13029-016-0060-z](https://doi.org/10.1186/s13029-016-0060-z).\n\n* Validation paper, including description of novel additions, such as off-target\n  support, tangent normalization and tweaks to the likelihood model:\n\n    Oh S, Geistlinger L, Ramos M, Morgan M,  Waldron L, Riester M (2020).\n    Reliable analysis of clinical tumor-only whole exome sequencing data.\n    _JCO Clinical Cancer Informatics_. doi: [10.1200/CCI.19.00130](https://doi.org/10.1200/CCI.19.00130);  \n    _bioRxiv_. doi: [10.1101/552711](https://doi.org/10.1101/552711)\n\n## Selected citations\n\nPereira et al. (2021). \"Cell-free DNA captures tumor heterogeneity and driver\nalterations in rapid autopsies with pre-treated metastatic cancer\". _Nature\nCommunications_. doi:\n[10.1038/s41467-021-23394-4](https://doi.org/10.1038/s41467-021-23394-4).\n\nDummer et al. (2020). \"Combined PD-1, BRAF and MEK inhibition in advanced\nBRAF-mutant melanoma: safety run-in and biomarker cohorts of COMBI-i\". _Nature\nMedicine_. doi: [10.1038/s41591-020-1082-2](https://doi.org/10.1038/s41591-020-1082-2).\n\nBertucci et al. (2019). \"Genomic characterization of metastatic breast cancers\".\n_Nature_. doi: [10.1038/s41586-019-1056-z](https://doi.org/10.1038/s41586-019-1056-z).\n\nDagogo-Jack et al. (2018). \"Tracking the evolution of resistance to ALK tyrosine kinase\ninhibitors through longitudinal analysis of circulating tumor DNA\". _JCO\nPrecision Oncology_. doi:\n[10.1200/PO.17.00160](https://doi.org/10.1200/PO.17.00160).\n\nOrlando et al. (2018). \"Genetic mechanisms of target antigen loss in CAR19 therapy of\nacute lymphoblastic leukemia\". _Nature Medicine_.\ndoi: [10.1038/s41591-018-0146-z](https://doi.org/10.1038/s41591-018-0146-z).\n\nPal et al. (2018). \"Efficacy of BGJ398, a fibroblast growth factor receptor 1-3\ninhibitor, in patients with previously treated advanced urothelial carcinoma\nwith FGFR3 alterations\". _Cancer Discovery_. doi:\n[10.1158/2159-8290.CD-18-0229](https://doi.org/10.1158/2159-8290.CD-18-0229).\n\nPitt et al. (2018). \"Characterization of Nigerian breast cancer reveals\nprevalent homologous recombination deficiency and aggressive molecular\nfeatures\". _Nature Communications_. doi:\n[10.1038/s41467-018-06616-0](https://doi.org/10.1038/s41467-018-06616-0).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flima1%2Fpurecn","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flima1%2Fpurecn","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flima1%2Fpurecn/lists"}