{ "_id": "6a15454eacfb0bcc41d5728c", "Package": "tradeSeq", "Type": "Package", "Title": "trajectory-based differential expression analysis for sequencing\ndata", "Date": "2019-03-17", "Version": "1.13.13", "Authors@R": "c(person(\"Zaoqu\", \"Liu\", role = c(\"aut\", \"cre\"),\nemail = \"liuzaoqu@163.com\",\ncomment = c(ORCID = \"0000-0002-0452-742X\")),\nperson(\"Koen\", \"Van den Berge\", role = c(\"aut\"),\nemail = \"koen.vandenberge@ugent.be\"),\nperson(\"Hector\", \"Roux de Bezieux\", role = c(\"aut\"),\nemail = \"hector.rouxdebezieux@berkeley.edu\",\ncomment = c(ORCID = \"0000-0002-1489-8339\")),\nperson(\"Kelly\",\"Street\", role = c(\"aut\",\"ctb\")),\nperson(\"Lieven\",\"Clement\", role=c(\"aut\",\"ctb\")),\nperson(\"Sandrine\",\"Dudoit\", role=\"ctb\"))", "Description": "tradeSeq provides a flexible method for fitting regression\nmodels that can be used to find genes that are differentially\nexpressed along one or multiple lineages in a trajectory. Based\non the fitted models, it uses a variety of tests suited to\nanswer different questions of interest, e.g. the discovery of\ngenes for which expression is associated with pseudotime, or\nwhich are differentially expressed (in a specific region) along\nthe trajectory. It fits a negative binomial generalized\nadditive model (GAM) for each gene, and performs inference on\nthe parameters of the GAM.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "false", "URL": "https://zaoqu-liu.github.io/tradeSeq,\nhttps://github.com/Zaoqu-Liu/tradeSeq", "Collate": "'AllGenerics.R' 'utils.R' 'associationTest.R' 'cascade.R'\n'clusterExpressionPatterns.R' 'conditionTest.R' 'data.R'\n'diffEndTest.R' 'earlyDETest.R' 'evaluateK.R' 'fitGAM.R'\n'getSmootherPvalues.R' 'getSmootherTestStats.R' 'nknots.R'\n'patternTest.R' 'plotGeneCount.R' 'plotSmoothers.R'\n'predictCells.R' 'predictSmooth.R' 'startVsEndTest.R'", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "biocViews": "Clustering, Regression, TimeCourse, DifferentialExpression,\nGeneExpression, RNASeq, Sequencing, Software, SingleCell,\nTranscriptomics, MultipleComparison, Visualization", "BugReports": "https://github.com/Zaoqu-Liu/tradeSeq/issues", "Config/pak/sysreqs": "libglpk-dev libxml2-dev 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