{ "_id": "6a10247bacfb0bcc41c8dc85", "Package": "BASiCS", "Type": "Package", "Title": "Bayesian Analysis of Single-Cell Sequencing data", "Version": "2.25.0", "Date": "2026-04-14", "Authors@R": "c(person(\"Catalina\", \"Vallejos\", role=c(\"aut\", \"cre\"),\nemail=\"catalina.vallejos@igmm.ed.ac.uk\",\ncomment=c(ORCID = \"0000-0003-3638-1960\")),\nperson(\"Nils\", \"Eling\", role=c(\"aut\")),\nperson(\"Alan\", \"O'Callaghan\", role = c(\"aut\")),\nperson(\"Sylvia\", \"Richardson\", role = c(\"ctb\")),\nperson(\"John\", \"Marioni\", role=c(\"ctb\")))", "Description": "Single-cell mRNA sequencing can uncover novel cell-to-cell\nheterogeneity in gene expression levels in seemingly\nhomogeneous populations of cells. However, these experiments\nare prone to high levels of technical noise, creating new\nchallenges for identifying genes that show genuine\nheterogeneous expression within the population of cells under\nstudy. BASiCS (Bayesian Analysis of Single-Cell Sequencing\ndata) is an integrated Bayesian hierarchical model to perform\nstatistical analyses of single-cell RNA sequencing datasets in\nthe context of supervised experiments (where the groups of\ncells of interest are known a priori, e.g. experimental\nconditions or cell types). BASiCS performs built-in data\nnormalisation (global scaling) and technical noise\nquantification (based on spike-in genes). BASiCS provides an\nintuitive detection criterion for highly (or lowly) variable\ngenes within a single group of cells. Additionally, BASiCS can\ncompare gene expression patterns between two or more\npre-specified groups of cells. Unlike traditional differential\nexpression tools, BASiCS quantifies changes in expression that\nlie beyond comparisons of means, also allowing the study of\nchanges in cell-to-cell heterogeneity. The latter can be\nquantified via a biological over-dispersion parameter that\nmeasures the excess of variability that is observed with\nrespect to Poisson sampling noise, after normalisation and\ntechnical noise removal. Due to the strong mean/over-dispersion\nconfounding that is typically observed for scRNA-seq datasets,\nBASiCS also tests for changes in residual over-dispersion,\ndefined by residual values with respect to a global\nmean/over-dispersion trend.", "License": "GPL-3", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, Normalization, Sequencing, RNASeq, Software,\nGeneExpression, Transcriptomics, SingleCell,\nDifferentialExpression, Bayesian, CellBiology, ImmunoOncology", "NeedsCompilation": "yes", "URL": "https://github.com/catavallejos/BASiCS", "BugReports": "https://github.com/catavallejos/BASiCS/issues", "RoxygenNote": "7.3.3", "Encoding": "UTF-8", "LazyData": "false", "Config/testthat/edition": "3", "Collate": "'AllClasses.R' 'AllGenerics.R' 'BASiCS_CalculateERCC.R'\n'BASiCS_CorrectOffset.R' 'BASiCS_DenoisedCounts.R'\n'BASiCS_DenoisedRates.R' 'BASiCS_DetectHVG_LVG.R'\n'BASiCS_DiagHist.R' 'BASiCS_DiagPlot.R'\n'BASiCS_DivideAndConquer.R' 'BASiCS_Draw.R'\n'BASiCS_EffectiveSize.R' 'BASiCS_Filter.R' 'BASiCS_LoadChain.R'\n'BASiCS_MCMC.R' 'BASiCS_MockSCE.R' 'BASiCS_Package.R'\n'BASiCS_PlotDE.R' 'BASiCS_PlotOffset.R' 'BASiCS_PlotVG.R'\n'BASiCS_PlotVarianceDecomp.R' 'BASiCS_PriorParam.R'\n'BASiCS_ShowFit.R' 'BASiCS_Sim.R' 'BASiCS_TestDE.R'\n'BASiCS_VarThresholdSearchHVG_LVG.R' 'BASiCS_VarianceDecomp.R'\n'HiddenBASiCS_Sim.R' 'HiddenHeaderBASiCS_Sim.R'\n'HiddenHeaderTest_DE.R' 'HiddenVarDecomp.R' 'utils_Misc.R'\n'Methods.R' 'RcppExports.R' 'data.R' 'makeExampleBASiCS_Data.R'\n'newBASiCS_Chain.R' 'newBASiCS_Data.R' 'utils_Data.R'\n'utils_DivideAndConquer.R' 'utils_MCMC.R' 'utils_Store.R'\n'utils_Tests.R' 'utils_VG.R' 'welcome.R'", "Config/pak/sysreqs": "cmake libglpk-dev make libicu-dev libuv1-dev\nlibxml2-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:46:30 UTC", "RemoteUrl": "https://github.com/bioc/BASiCS", "RemoteRef": "HEAD", "RemoteSha": "12c423b8116afefb47050d28cf726c5a266ef098", "Packaged": { "Date": "2026-05-13 09:48:47 UTC", "User": "root" }, "Author": "Catalina Vallejos [aut, cre] (ORCID:\n),\nNils Eling [aut],\nAlan O'Callaghan [aut],\nSylvia Richardson [ctb],\nJohn Marioni [ctb]", "Maintainer": "Catalina Vallejos ", "MD5sum": "575779b9bee6c96af43379d6343465ef", "_user": "bioc", "_type": "src", "_file": "BASiCS_2.25.0.tar.gz", "_fileid": "35807afaa9ff69c4555ddbb1eeeae2925cedf376f12e07473b1b755fd364ac0b", "_filesize": 3476451, "_sha256": "35807afaa9ff69c4555ddbb1eeeae2925cedf376f12e07473b1b755fd364ac0b", "_created": "2026-05-13T09:48:47.000Z", "_published": "2026-05-22T09:40:11.859Z", "_jobs": [ { "job": 77354227032, "time": 278, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "6966941629" }, { "job": 77354226689, "time": 539, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "6967033598" }, { "job": 77354226878, "time": 646, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6967074767" }, { "job": 77354226723, "time": 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