{ "_id": "6a1b03701d7bb097a0a01e2f", "Package": "SCOPE", "Type": "Package", "Title": "A normalization and copy number estimation method for\nsingle-cell DNA sequencing", "Version": "1.25.0", "Author": "Rujin Wang, Danyu Lin, Yuchao Jiang", "Maintainer": "Rujin Wang ", "Description": "Whole genome single-cell DNA sequencing (scDNA-seq)\nenables characterization of copy number profiles at the\ncellular level. This circumvents the averaging effects\nassociated with bulk-tissue sequencing and has increased\nresolution yet decreased ambiguity in deconvolving cancer\nsubclones and elucidating cancer evolutionary history.\nScDNA-seq data is, however, sparse, noisy, and highly variable\neven within a homogeneous cell population, due to the biases\nand artifacts that are introduced during the library\npreparation and sequencing procedure. Here, we propose SCOPE, a\nnormalization and copy number estimation method for scDNA-seq\ndata. The distinguishing features of SCOPE include: (i)\nutilization of cell-specific Gini coefficients for quality\ncontrols and for identification of normal/diploid cells, which\nare further used as negative control samples in a Poisson\nlatent factor model for normalization; (ii) modeling of GC\ncontent bias using an expectation-maximization algorithm\nembedded in the Poisson generalized linear models, which\naccounts for the different copy number states along the genome;\n(iii) a cross-sample iterative segmentation procedure to\nidentify breakpoints that are shared across cells from the same\ngenetic background.", "VignetteBuilder": "knitr", "biocViews": "SingleCell, Normalization, CopyNumberVariation, Sequencing,\nWholeGenome, Coverage, Alignment, QualityControl, DataImport,\nDNASeq", "License": "GPL-2", "LazyData": "true", "RoxygenNote": "6.1.1", "Encoding": "UTF-8", "Config/pak/sysreqs": "cmake make libbz2-dev liblzma-dev libuv1-dev\nlibxml2-dev libssl-dev libx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:51:50 UTC", "RemoteUrl": "https://github.com/bioc/SCOPE", "RemoteRef": "HEAD", "RemoteSha": "3cc19e682b10d081a198be19645cca91a77adecb", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 10:01:52 UTC", "User": "root" }, "MD5sum": "3c4d6fe0a048b1d71b9717aea9a08627", "_user": "bioc", "_type": "src", "_file": "SCOPE_1.25.0.tar.gz", "_fileid": "151dd3f83cbaabbc3b5b53a584b849b1974ba437689489e19bb15d75ed82b14d", "_filesize": 363962, "_sha256": "151dd3f83cbaabbc3b5b53a584b849b1974ba437689489e19bb15d75ed82b14d", "_created": "2026-05-30T10:01:52.000Z", "_published": "2026-05-30T15:34:08.083Z", "_jobs": [ { "job": 78641390315, "time": 412, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7307646719" }, { "job": 78641390312, "time": 662, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7307671322" }, { "job": 78641390318, "time": 630, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7307668733" }, { "job": 78641390304, "time": 321, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7309269681" }, { "job": 78641390327, "time": 410, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7309282466" }, { "job": 78640055684, "time": 779, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307377391" }, { "job": 78641390307, "time": 331, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307638678" }, { "job": 78641390317, "time": 479, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7307654132" }, { "job": 78641390310, "time": 578, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7307663621" }, { "job": 78641390316, "time": 466, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7307652431" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677060093", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/SCOPE", "_commit": { "id": "3cc19e682b10d081a198be19645cca91a77adecb", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380710 }, "_maintainer": { "name": "Rujin Wang", "email": "rujin@email.unc.edu" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "GenomicRanges", "role": "Depends" }, { "package": "IRanges", "role": "Depends" }, { "package": "Rsamtools", "role": "Depends" }, { "package": "GenomeInfoDb", "role": "Depends" }, { "package": "BSgenome.Hsapiens.UCSC.hg19", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "DescTools", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "gplots", "role": "Imports" }, { "package": "foreach", "role": "Imports" }, { "package": "parallel", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "DNAcopy", "role": "Imports" }, { "package": "BSgenome", "role": "Imports" }, { "package": "Biostrings", "role": "Imports" }, { "package": "BiocGenerics", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "WGSmapp", "role": "Suggests" }, { "package": "BSgenome.Hsapiens.UCSC.hg38", "role": "Suggests" }, { "package": "BSgenome.Mmusculus.UCSC.mm10", "role": "Suggests" }, { "package": "testthat", "version": ">= 2.1.0", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.25.0", "bioc": "3.24" }, { "branch": "release", "version": "1.24.0", "bioc": "3.23" } ], "_topics": [ "singlecell", "normalization", "copynumbervariation", "sequencing", "wholegenome", "coverage", "alignment", "qualitycontrol", "dataimport", "dnaseq" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 369, "source": "https://www.bioconductor.org/packages/stats/bioc/SCOPE" }, "_mentions": 56, "_searchresults": 114, "_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/readme.html", "extra/readme.md", "extra/SCOPE.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "get_bam_bed", "get_coverage_scDNA", "get_gc", "get_gini", "get_mapp", "get_samp_QC", "initialize_ploidy", "initialize_ploidy_group", "normalize_codex2_ns_noK", "normalize_scope", "normalize_scope_foreach", "normalize_scope_group", "perform_qc", "plot_EM_fit", "plot_iCN", "segment_CBScs" ], "_datasets": [ { "name": "coverageObj.scopeDemo", "title": "Pre-stored coverageObj.scope data for demonstration purposes", "object": "coverageObj.scopeDemo", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "iCN_sim", "title": "A post cross-sample segmentation integer copy number matrix returned by SCOPE in the demo", "object": "iCN_sim", "class": [ "matrix", "array" ], "fields": [ "cell1", "cell2", "cell3", "cell4", "cell5" ], "rows": 1544, "table": true, "tojson": true }, { "name": "normObj.scopeDemo", "title": "Pre-stored normObj.scope data for demonstration purposes", "object": "normObj.scopeDemo", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "QCmetric.scopeDemo", "title": "Pre-stored QCmetric data for demonstration purposes", "object": "QCmetric.scopeDemo", "class": [ "matrix", "array" ], "fields": [ "readlength", "total", "mapped", "mapped_prop", "non_dup", "non_dup_prop", "mapq20", "mapq20_prop" ], "rows": 3, "table": true, "tojson": true }, { "name": "ref_sim", "title": "A reference genome in the toy dataset", "object": "demo", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "ref.scopeDemo", "title": "Pre-stored 500kb-size reference genome for demonstration purposes", "object": "ref.scopeDemo", "class": [ "GRanges" ], "fields": [], "table": false, "tojson": false }, { "name": "Y_sim", "title": "A read count matrix in the toy dataset", "object": "demo", "class": [ "matrix", "array" ], "fields": [ "cell1", "cell2", "cell3", "cell4", "cell5" ], "rows": 1544, "table": true, "tojson": true } ], "_help": [ { "page": "coverageObj.scopeDemo", "title": "Pre-stored coverageObj.scope data for demonstration purposes", "topics": [ "coverageObj.scopeDemo" ] }, { "page": "get_bam_bed", "title": "Get bam file directories, sample names, and whole genomic bins", "topics": [ "get_bam_bed" ] }, { "page": "get_coverage_scDNA", "title": "Get read coverage from single-cell DNA sequencing", "topics": [ "get_coverage_scDNA" ] }, { "page": "get_gc", "title": "Compute GC content", "topics": [ "get_gc" ] }, { "page": "get_gini", "title": "Compute Gini coefficients for single cells", "topics": [ "get_gini" ] }, { "page": "get_mapp", "title": "Compute mappability", "topics": [ "get_mapp" ] }, { "page": "get_samp_QC", "title": "Get QC metrics for single cells", "topics": [ "get_samp_QC" ] }, { "page": "iCN_sim", "title": "A post cross-sample segmentation integer copy number matrix returned by SCOPE in the demo", "topics": [ "iCN_sim" ] }, { "page": "initialize_ploidy", "title": "Ploidy pre-initialization", "topics": [ "initialize_ploidy" ] }, { "page": "initialize_ploidy_group", "title": "Group-wise ploidy pre-initialization", "topics": [ "initialize_ploidy_group" ] }, { "page": "normalize_codex2_ns_noK", "title": "Normalization of read depth without latent factors under the case-control setting", "topics": [ "normalize_codex2_ns_noK" ] }, { "page": "normalize_scope", "title": "Normalization of read depth with latent factors using Expectation-Maximization algorithm under the case-control setting", "topics": [ "normalize_scope" ] }, { "page": "normalize_scope_foreach", "title": "Normalization of read depth with latent factors using Expectation-Maximization algorithm under the case-control setting in parallel", "topics": [ "normalize_scope_foreach" ] }, { "page": "normalize_scope_group", "title": "Group-wise normalization of read depth with latent factors using Expectation-Maximization algorithm and shared clonal memberships", "topics": [ "normalize_scope_group" ] }, { "page": "normObj.scopeDemo", "title": "Pre-stored normObj.scope data for demonstration purposes", "topics": [ "normObj.scopeDemo" ] }, { "page": "perform_qc", "title": "Quality control for cells and bins", "topics": [ "perform_qc" ] }, { "page": "plot_EM_fit", "title": "Visualize EM fitting for each cell.", "topics": [ "plot_EM_fit" ] }, { "page": "plot_iCN", "title": "Plot post-segmentation copy number profiles of integer values", "topics": [ "plot_iCN" ] }, { "page": "QCmetric.scopeDemo", "title": "Pre-stored QCmetric data for demonstration purposes", "topics": [ "QCmetric.scopeDemo" ] }, { "page": "ref_sim", "title": "A reference genome in the toy dataset", "topics": [ "ref_sim" ] }, { "page": "ref.scopeDemo", "title": "Pre-stored 500kb-size reference genome for demonstration purposes", "topics": [ "ref.scopeDemo" ] }, { "page": "segment_CBScs", "title": "Cross-sample segmentation", "topics": [ "segment_CBScs" ] }, { "page": "Y_sim", "title": "A read count matrix in the toy dataset", "topics": [ "Y_sim" ] } ], "_readme": "https://github.com/bioc/SCOPE/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "boot", "BSgenome", "BSgenome.Hsapiens.UCSC.hg19", "caTools", "cellranger", "cigarillo", "class", "cli", "clipr", "codetools", "cpp11", "crayon", "curl", "data.table", "DelayedArray", "DescTools", "DNAcopy", "doParallel", "e1071", "Exact", "expm", "forcats", "foreach", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicRanges", "gld", "glue", "gplots", "gtools", "haven", "hms", "httr", "IRanges", "iterators", "jsonlite", "KernSmooth", "lambda.r", "lattice", "lifecycle", "lmom", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "mime", "mvtnorm", "openssl", "pillar", "pkgconfig", "prettyunits", "progress", "proxy", "R6", "RColorBrewer", "Rcpp", "RCurl", "readr", "readxl", "rematch", "restfulr", "Rhtslib", "rjson", "rlang", "rootSolve", "Rsamtools", "rstudioapi", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "sys", "tibble", "tidyselect", "tzdb", "UCSC.utils", "utf8", "vctrs", "vroom", "withr", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "SCOPE_vignette.Rmd", "filename": "SCOPE_vignette.html", "title": "SCOPE: Single-cell Copy Number Estimation", "author": "Rujin Wang, Danyu Lin, Yuchao Jiang", "engine": "knitr::rmarkdown", "headings": [ "1. Overview of analysis pipeline", "1.1 Introduction", "1.2 Bioinformatic pre-processing", "2. Pre-computation and Quality Control", "2.1 Pre-preparation", "2.2 Getting GC content and mappability", "2.3 Getting coverage", "2.4 Quality control", "3. Running SCOPE", "3.1 Gini coefficient", "3.2 Running SCOPE with negative control samples", "3.3 Cross-sample segmentation by SCOPE", "3.4 Visualization", "Session information" ], "created": "2019-09-09 15:57:10", "modified": "2021-07-14 20:08:11", "commits": 12 } ], "_score": 6.056904851336473, "_indexed": true, "_nocasepkg": "scope", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T10:51:29.000Z", "distro": "noble", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "0d24a33cde68176954ef14935292206fa0edccdc88ee412fa0f41ba74819e54d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677060093" }, { "r": "4.6.0", "os": "linux", "version": "1.25.0", "date": "2026-05-30T10:51:30.000Z", "distro": "noble", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "76514a2bb87b40e48d555d7edb115565b096cf819e7d619c5b0fe30ac8a5fc6e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677060093" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-05-30T15:29:28.000Z", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "5c95ac4106e914d4bf64689b38e1156316628d43255587a1f991161f18fc4d05", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677060093" }, { "r": "4.6.0", "os": "mac", "version": "1.25.0", "date": "2026-05-30T15:30:40.000Z", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "081cbc6bb189e7180da911476a9a9c0aad0e4af258bab2cd8984fc792d4303a0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677060093" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.0", "date": "2026-05-30T10:50:09.000Z", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "1365f9b699293b71738e76bcd83ccdf40bd85cddd8906f4f137f97c157162fbe", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677060093" }, { "r": "4.7.0", "os": "win", "version": "1.25.0", "date": "2026-05-30T10:48:10.000Z", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "4913baa1efbab4a13770a791dc1615de25565471d0d2cde06f924375ac8b8584", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677060093" }, { "r": "4.5.3", "os": "win", "version": "1.25.0", "date": "2026-05-30T10:49:11.000Z", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "cb0bc116ac79923f8aca5b70dfe8cf90a75a90dac38831969e265955283fa76f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677060093" }, { "r": "4.6.0", "os": "win", "version": "1.25.0", "date": "2026-05-30T10:48:20.000Z", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "81272bf4cb1e4455409190aa7a58335dff9bc3661b20a8d318a32eb2c7703a66", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677060093" } ] }