{ "_id": "6aabcf5e3d719c1f8406f297", "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": "2026-09-17 10:13:50 UTC", "User": "root" }, "_user": "bioc", "_type": "src", "_file": "SCOPE_1.25.0.tar.gz", "_fileid": "https://r2.ropensci.org/4062f92421a4ecd20522c1b28089bb46a08525c8dd7abb862d6b531963d161d9", "_filesize": 368158, "_sha256": "4062f92421a4ecd20522c1b28089bb46a08525c8dd7abb862d6b531963d161d9", "_expires": "2026-12-26T11:30:36.000Z", "_created": "2026-09-17T10:13:50.000Z", "_published": "2026-09-17T11:30:38.688Z", "_bioccheck": { "error": 1, "warning": 1, "note": 12 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/bioc/actions/runs/35208450022", "_status": "success", "_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": "resolute", "_jobs": [ { "job": 105163112737, "time": 368, "config": "bioc-checks", "r": "4.6.1", "check": "ERROR", "artifact": "10491068441" }, { "job": 105163112705, "time": 479, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10491676585" }, { "job": 105163112839, "time": 514, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10491369544" }, { "job": 105163112690, "time": 367, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10495265622" }, { "job": 105163112715, "time": 444, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10495016550" }, { "job": 105159977040, "time": 645, "config": "source", "r": 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"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" ] } ], 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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": 6.2552725051033065, "_indexed": true, "_nocasepkg": "scope", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.25.0", "date": "2026-09-17T10:19:28.000Z", "distro": "resolute", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "https://r2.ropensci.org/321abfb21418cd0293331681e065b471c862406aac2b97bcc4ce83a9818db7c3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35208450022" }, { "r": "4.6.1", "os": "linux", "version": "1.25.0", "date": "2026-09-17T10:19:49.000Z", "distro": "resolute", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "https://r2.ropensci.org/a7e9f0901183e4988fcfdc57225f82d5c57b54536e61853b5aa52227499204d5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35208450022" }, { "r": "4.5.3", "os": "mac", "version": "1.25.0", "date": "2026-09-17T11:25:47.000Z", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "https://r2.ropensci.org/a4f75205646bb8960beb16be45dc9b1e0ea57fa5e29983f9eb2612eed5badb5a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35208450022" }, { "r": "4.6.1", "os": "mac", "version": "1.25.0", "date": "2026-09-17T11:26:29.000Z", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "https://r2.ropensci.org/d6963d9b37652c2821b88454074e4b76b04ac9e27795d079755ce8b838123201", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35208450022" }, { "r": "4.6.0", "os": "wasm", "version": "1.25.0", "date": "2026-09-17T10:19:31.000Z", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "https://r2.ropensci.org/97defb75ea528f14f3f1a31ce4403fb7bb2de9fdf3195675c5d6af8a748d0358", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35208450022" }, { "r": "4.7.0", "os": "win", "version": "1.25.0", "date": "2026-09-17T10:17:36.000Z", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "https://r2.ropensci.org/23804cf92b76f462aa001a90100720c4d96288efc405ec3bb9e586371de33f42", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35208450022" }, { "r": "4.5.3", "os": "win", "version": "1.25.0", "date": "2026-09-17T10:18:25.000Z", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "https://r2.ropensci.org/e1a90b328a36ed4093456c63e88626ed4da84bbc71edfcad3ed2ecf78f697f4c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35208450022" }, { "r": "4.6.1", "os": "win", "version": "1.25.0", "date": "2026-09-17T10:18:00.000Z", "commit": "3cc19e682b10d081a198be19645cca91a77adecb", "fileid": "https://r2.ropensci.org/3362df389771c16f68c4c47edfb27ed2a5ae8f1dc33c33b21a4c91f738f6d726", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/35208450022" } ] }