{ "_id": "6a1be3b71d7bb097a0a191b0", "Package": "Oscope", "Type": "Package", "Title": "Oscope - A statistical pipeline for identifying oscillatory\ngenes in unsynchronized single cell RNA-seq", "Version": "1.43.0", "Date": "2015-7-28", "Author": "Ning Leng", "Maintainer": "Ning Leng ", "Description": "Oscope is a statistical pipeline developed to identifying\nand recovering the base cycle profiles of oscillating genes in\nan unsynchronized single cell RNA-seq experiment. The Oscope\npipeline includes three modules: a sine model module to search\nfor candidate oscillator pairs; a K-medoids clustering module\nto cluster candidate oscillators into groups; and an extended\nnearest insertion module to recover the base cycle order for\neach oscillator group.", "License": "Artistic-2.0", "Collate": "'AbsCor.R' 'NormForSine.R' 'SineFun.R' 'FormatSineOut.R'\n'Opt2Shift.R' 'SineOptim.R' 'PipeR.R' 'ImpShift.R'\n'PipeShiftCDF.R' 'scanK.R' 'NISFun.R' 'CalcMV.R' 'OscopeKM.R'\n'OscopeENI.R' 'OscopeSine.R' 'FlagCluster.R' 'PermuCut.R'", "BuildVignettes": "yes", "biocViews": "ImmunoOncology, StatisticalMethod,RNASeq, Sequencing,\nGeneExpression", "NeedsCompilation": "no", "Config/pak/sysreqs": "cmake make libuv1-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:41:38 UTC", "RemoteUrl": "https://github.com/bioc/Oscope", "RemoteRef": "HEAD", "RemoteSha": "4944b6cdfcd685b25149ded5982b26fdebb175b3", "Packaged": { "Date": "2026-05-31 06:35:24 UTC", "User": "root" }, "MD5sum": "bb89a1df405caba114648c5cdaffdbea", "_user": "bioc", "_type": "src", "_file": "Oscope_1.43.0.tar.gz", "_fileid": "7596ba71f9b8ae5bfffca7f79e1c74e15a64ba8fe8725b616c054d03ed2831aa", "_filesize": 1347509, "_sha256": "7596ba71f9b8ae5bfffca7f79e1c74e15a64ba8fe8725b616c054d03ed2831aa", "_created": "2026-05-31T06:35:24.000Z", "_published": "2026-05-31T07:31:03.888Z", "_jobs": [ { "job": 78705954291, "time": 137, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7314485870" }, { "job": 78705954281, "time": 198, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7314492821" }, { "job": 78705954288, "time": 220, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7314495297" }, { "job": 78705954283, "time": 110, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7314828755" }, { "job": 78705954279, "time": 99, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7314825363" }, { "job": 78705611933, "time": 344, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7314469560" }, { "job": 78705954275, "time": 130, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7314485236" }, { "job": 78705954289, "time": 129, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7314485056" }, { "job": 78705954292, "time": 118, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7314483708" }, { "job": 78705954287, "time": 209, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7314494089" } ], "_bioccheck": { "error": 1, "warning": 3, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26705396382", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/Oscope", "_commit": { "id": "4944b6cdfcd685b25149ded5982b26fdebb175b3", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380098 }, "_maintainer": { "name": "Ning Leng", "email": "lengning1@gmail.com", "login": "lengning", "description": "", "uuid": 11322800 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "EBSeq", "role": "Depends" }, { "package": "cluster", "role": "Depends" }, { "package": "testthat", "role": "Depends" }, { "package": "BiocParallel", "role": "Depends" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.43.0", "bioc": "3.24" }, { "branch": "release", "version": "1.42.0", "bioc": "3.23" } ], "_topics": [ "immunooncology", "statisticalmethod", "rnaseq", "sequencing", "geneexpression" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 514, "source": "https://www.bioconductor.org/packages/stats/bioc/Oscope" }, "_mentions": 11, "_searchresults": 16, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/Oscope.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "AbsCor", "CalcMV", "FlagCluster", "FormatSineOut", "ImpShift", "NISFun", "NormForSine", "Opt2Shift", "OscopeENI", "OscopeKM", "OscopeSine", "PermuCut", "PipeR", "PipeShiftCDF", "scanK", "SineFun", "SineOptim" ], "_datasets": [ { "name": "OscopeExampleData", "title": "Simulated gene level data set with 600 genes and 30 cells.", "object": "OscopeExampleData", "file": "OscopeExampleData.rda", "class": [ "matrix", "array" ], "fields": [ "S1", "S2", "S3", "S4", "S5", "S6", "S7", "S8", "S9", "S10", "S11", "S12", "S13", "S14", "S15", "S16", "S17", "S18", "S19", "S20", "S21", "S22", "S23", "S24", "S25", "S26", "S27", "S28", "S29", "S30" ], "rows": 500, "table": true, "tojson": true } ], "_help": [ { "page": "Oscope-package", "title": "Oscope - A statistical pipeline for identifying oscillatory genes in unsynchronized single cell RNA-seq", "topics": [ "Oscope-package", "Oscope" ] }, { "page": "AbsCor", "title": "Calculate absolute correlations among gene pairs", "topics": [ "AbsCor" ] }, { "page": "CalcMV", "title": "Calculate estimated mean and variance of RNA-Seq data", "topics": [ "CalcMV" ] }, { "page": "FlagCluster", "title": "Flag gene clusters with small within-cluster phase differences and/or small within-cluster sine scores", "topics": [ "FlagCluster" ] }, { "page": "FormatSineOut", "title": "Format SinFun outputs from lists to matrix", "topics": [ "FormatSineOut" ] }, { "page": "ImpShift", "title": "Search for the optimal sample order by using the Extended Nearest Insertion", "topics": [ "ImpShift" ] }, { "page": "NISFun", "title": "Run Extended Nearest Insertion and 2-opt on a gene cluster identified by OscopeKM function", "topics": [ "NISFun" ] }, { "page": "NormForSine", "title": "Rescale the gene/isoform expression matrix", "topics": [ "NormForSine" ] }, { "page": "Opt2Shift", "title": "Run the 2-opt algorithm to improve the optimal order searching of the Extended Nearest Insertion", "topics": [ "Opt2Shift" ] }, { "page": "OscopeENI", "title": "Search for the optimal sample order for different gene clusters", "topics": [ "OscopeENI" ] }, { "page": "OscopeExampleData", "title": "Simulated gene level data set with 600 genes and 30 cells.", "topics": [ "OscopeExampleData" ] }, { "page": "OscopeKM", "title": "Oscope K medoid module", "topics": [ "OscopeKM" ] }, { "page": "OscopeSine", "title": "Apply sine model on the full set of genes or isoforms", "topics": [ "OscopeSine" ] }, { "page": "PermuCut", "title": "Define sine scroe cutoff using permuted data", "topics": [ "PermuCut" ] }, { "page": "PipeR", "title": "Calculate residual of polynomial fit", "topics": [ "PipeR" ] }, { "page": "PipeShiftCDF", "title": "Calculate residual of the sliding polynomial regression", "topics": [ "PipeShiftCDF" ] }, { "page": "scanK", "title": "Run k-medoid algorithm with varying k on similarity matrix", "topics": [ "scanK" ] }, { "page": "SineFun", "title": "Apply sine model on one particular gene vs. other genes", "topics": [ "SineFun" ] }, { "page": "SineOptim", "title": "Function for searching optimal phase shift", "topics": [ "SineOptim" ] } ], "_rundeps": [ "BH", "BiocParallel", "bitops", "blockmodeling", "brio", "callr", "caTools", "cli", "cluster", "codetools", "cpp11", "crayon", "desc", "diffobj", "EBSeq", "evaluate", "formatR", "fs", "futile.logger", "futile.options", "glue", "gplots", "gtools", "jsonlite", "KernSmooth", "lambda.r", "lattice", "lifecycle", "magrittr", "Matrix", "pkgbuild", "pkgload", "praise", "processx", "ps", "R6", "Rcpp", "RcppEigen", "rlang", "rprojroot", "snow", "testthat", "waldo", "withr" ], "_vignettes": [ { "source": "Oscope_vignette.Rnw", "filename": "Oscope_vignette.pdf", "title": "Oscope_vigette", "engine": "utils::Sweave", "headings": [], "created": "2015-07-30 18:18:36", "modified": "2015-07-30 18:18:36", "commits": 1 } ], "_score": 4.982271233039569, "_indexed": true, "_nocasepkg": "oscope", "_universes": [ "bioc", "lengning" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.43.0", "date": "2026-05-31T06:38:09.000Z", "distro": "noble", "commit": "4944b6cdfcd685b25149ded5982b26fdebb175b3", "fileid": "617ca497788f357f68d54290a7e6785a81fcf2ebed686d296259a218c1952e35", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705396382" }, { "r": "4.6.0", "os": "linux", "version": "1.43.0", "date": "2026-05-31T06:38:32.000Z", "distro": "noble", "commit": "4944b6cdfcd685b25149ded5982b26fdebb175b3", "fileid": "7092d72d9865cf45b2d0e9a10f9080b4fab3cfe5d22da12f7a6607bf364b1186", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705396382" }, { "r": "4.5.3", "os": "mac", "version": "1.43.0", "date": "2026-05-31T07:30:21.000Z", "commit": "4944b6cdfcd685b25149ded5982b26fdebb175b3", "fileid": "803fe24378ccb96ecad6d23945b231cb196af4ffb29142e60ee4529fa758140d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705396382" }, { "r": "4.6.0", "os": "mac", "version": "1.43.0", "date": "2026-05-31T07:29:54.000Z", "commit": "4944b6cdfcd685b25149ded5982b26fdebb175b3", "fileid": "cee0d52c4da85f9b94f035e54a3d3dea16552ab8bce7b8ab39fa454c668ec219", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705396382" }, { "r": "4.6.0", "os": "wasm", "version": "1.43.0", "date": "2026-05-31T06:37:49.000Z", "commit": "4944b6cdfcd685b25149ded5982b26fdebb175b3", "fileid": "3258a3bab9164215ec0aa3786c231d8e17b6f17a4ffd46eacc3dfe6696f26728", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705396382" }, { "r": "4.7.0", "os": "win", "version": "1.43.0", "date": "2026-05-31T06:36:50.000Z", "commit": "4944b6cdfcd685b25149ded5982b26fdebb175b3", "fileid": "0474325d9a852d063bd557c340adc902daa261d701edf51c1d5249aa954c27eb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705396382" }, { "r": "4.5.3", "os": "win", "version": "1.43.0", "date": "2026-05-31T06:37:02.000Z", "commit": "4944b6cdfcd685b25149ded5982b26fdebb175b3", "fileid": "fb410930a487657d7556aa4ba0aa2abd824d3ec4821c1cdcfc90e03b612561cc", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705396382" }, { "r": "4.6.0", "os": "win", "version": "1.43.0", "date": "2026-05-31T06:38:12.000Z", "commit": "4944b6cdfcd685b25149ded5982b26fdebb175b3", "fileid": "90646fc1694cb272cde8d63484c7e49fc36bd19bb5c380358f0b37a2d417e4fe", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26705396382" } ] }