{ "_id": "6ad326bd2c5c76d3dd0c9b12", "Package": "COTAN", "Type": "Package", "Title": "COexpression Tables ANalysis", "Version": "2.13.1", "Authors@R": "c(\nperson(\"Galfrè\", \"Silvia Giulia\",email = \"silvia.galfre@di.unipi.it\", role=c(\"aut\",\"cre\"),comment = c(ORCID = \"0000-0002-2770-0344\")),\nperson(\"Morandin\",\"Francesco\", email = \"francesco.morandin@unipr.it\", role = \"aut\",comment = c(ORCID = \"0000-0002-2022-2300\")),\nperson(\"Fantozzi\", \"Marco\", email = \"marco.fantozzi@gmail.com\", role = \"aut\", comment = c(ORCID = \"0000-0002-0708-5495\")),\nperson(\"Pietrosanto\",\"Marco\", role = \"aut\",comment = c(ORCID = \"0000-0001-5129-6065\")),\nperson(\"Puttini\",\"Daniel\", role = \"aut\", comment = c(ORCID = \"0009-0006-8401-9949\")),\nperson(\"Priami\",\"Corrado\", role = \"aut\", comment = c(ORCID = \"0000-0002-3261-6235\")),\nperson(\"Cremisi\",\"Federico\", role = \"aut\",comment = c(ORCID = \"0000-0003-4925-2703\")),\nperson(\"Helmer-Citterich\",\"Manuela\", role = \"aut\",comment = c(ORCID = \"0000-0001-9530-7504\"))\n)", "Description": "Statistical and computational method to analyze the\nco-expression of gene pairs at single cell level. It provides\nthe foundation for single-cell gene interactome analysis. The\nbasic idea is studying the zero UMI counts' distribution\ninstead of focusing on positive counts; this is done with a\ngeneralized contingency tables framework. COTAN can effectively\nassess the correlated or anti-correlated expression of gene\npairs. It provides a numerical index related to the correlation\nand an approximate p-value for the associated independence\ntest. COTAN can also evaluate whether single genes are\ndifferentially expressed, scoring them with a newly defined\nglobal differentiation index. Moreover, this approach provides\nways to plot and cluster genes according to their co-expression\npattern with other genes, effectively helping the study of gene\ninteractions and becoming a new tool to identify cell-identity\nmarker genes.", "URL": "https://github.com/seriph78/COTAN", "BugReports": "https://github.com/seriph78/COTAN/issues", "License": "GPL-3", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "Language": "en-US", "biocViews": "SystemsBiology, Transcriptomics, GeneExpression, SingleCell,\nDifferentialExpression, Clustering, GPU", "VignetteBuilder": "knitr", "LazyData": "false", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev perl python3 libx11-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-20 13:05:30 UTC", "RemoteUrl": "https://github.com/bioc/COTAN", "RemoteRef": "HEAD", "RemoteSha": 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"page": "LoggingFunctions", "title": "Logging in the 'COTAN' package", "topics": [ "LoggingFunctions", "logThis", "setLoggingFile", "setLoggingLevel" ] }, { "page": "MultiThreading", "title": "Handling Multi-Core and GPU environments", "topics": [ "canUseTorch", "handleMultiCore", "MultiThreading" ] }, { "page": "NumericUtilities", "title": "Numeric Utilities", "topics": [ "calcDist", "dispersionBisection", "dispersionNewton", "funProbZero", "nuBisection", "NumericUtilities", "parallelDispersionBisection", "parallelDispersionNewton", "parallelNuBisection" ] }, { "page": "ParametersEstimations", "title": "Estimation of the 'COTAN' model's parameters", "topics": [ "estimateDispersionBisection", "estimateDispersionNuBisection", "estimateDispersionNuBisection,COTAN-method", "estimateDispersionNuNlminb", "estimateDispersionNuNlminb,COTAN-method", "estimateDispersionViaSolver", "estimateDispersionViaSolver,COTAN-method", "estimateLambdaLinear", "estimateLambdaLinear,COTAN-method", 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