{ "_id": "6a1ade871d7bb097a09ebb65", "Package": "Coralysis", "Type": "Package", "Title": "Coralysis sensitive identification of imbalanced cell types and\nstates in single-cell data via multi-level integration", "Version": "1.2.0", "Description": "Coralysis is an R package featuring a multi-level\nintegration algorithm for sensitive integration,\nreference-mapping, and cell-state identification in single-cell\ndata. The multi-level integration algorithm is inspired by the\nprocess of assembling a puzzle - where one begins by grouping\npieces based on low-to high-level features, such as color and\nshading, before looking into shape and patterns. This approach\nprogressively blends the batch effects and separates cell types\nacross multiple rounds of divisive clustering.", "Authors@R": "c(person(\"António\", \"Sousa\",\nemail = \"aggode@utu.fi\",\nrole=c(\"cre\", \"aut\"),\ncomment = c(ORCID = \"0000-0003-4779-6459\")),\nperson(\"Johannes\", \"Smolander\",\nrole=c(\"ctb\", \"aut\"),\ncomment = c(ORCID = \"0000-0003-3872-9668\")),\nperson(\"Sini\", \"Junttila\",\nrole=c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-3754-5584\")),\nperson(\"Laura L\", \"Elo\",\nrole=c(\"aut\"),\ncomment = c(ORCID = \"0000-0001-5648-4532\")))", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.2", "VignetteBuilder": "knitr", "biocViews": "SingleCell, RNASeq, Proteomics, Transcriptomics,\nGeneExpression, BatchEffect, Clustering, Annotation,\nClassification, DifferentialExpression, DimensionReduction,\nSoftware", "NeedsCompilation": "no", "URL": "https://github.com/elolab/Coralysis,\nhttps://elolab.github.io/Coralysis/", "BugReports": "https://github.com/elolab/Coralysis/issues", "Config/testthat/edition": "3", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev make\nlibharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev\nlibuv1-dev libwebp-dev libxml2-dev libssl-dev python3\nzlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 13:05:04 UTC", "RemoteUrl": "https://github.com/bioc/Coralysis", "RemoteRef": "RELEASE_3_23", "RemoteSha": "24c1814b73cad37b5e240754cc5c650e743e69fd", "Packaged": { "Date": "2026-05-30 09:12:57 UTC", "User": "root" }, "Author": "António Sousa [cre, aut] (ORCID:\n),\nJohannes Smolander [ctb, aut] (ORCID:\n),\nSini Junttila [aut] (ORCID: ),\nLaura L Elo [aut] (ORCID: )", "Maintainer": "António Sousa ", "MD5sum": "7f45defbfd1d2aef017e39059bf66b19", "_user": "bioc-release", "_type": "src", "_file": "Coralysis_1.2.0.tar.gz", "_fileid": "269931230dabb0e406f5000a7270df96012c89ba8c3f541476c163dcedd521a9", "_filesize": 11673577, "_sha256": "269931230dabb0e406f5000a7270df96012c89ba8c3f541476c163dcedd521a9", "_created": "2026-05-30T09:12:57.000Z", "_published": "2026-05-30T12:56:39.092Z", "_jobs": [ { "job": 78638925589, "time": 259, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307149056" }, { "job": 78638925597, "time": 659, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307186804" }, { "job": 78638925615, "time": 657, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307186943" }, { "job": 78638925618, "time": 400, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7308338801" }, { "job": 78638925613, "time": 299, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7308327949" }, { "job": 78638188175, "time": 857, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307094830" }, { "job": 78638925595, "time": 263, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307149345" }, { "job": 78638925604, "time": 1733, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7307291659" }, { "job": 78638925602, "time": 1727, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7307290312" }, { "job": 78638925611, "time": 1728, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7307291245" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679830194", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/Coralysis", "_commit": { "id": "24c1814b73cad37b5e240754cc5c650e743e69fd", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to even y prior to creation of RELEASE_3_23 branch\n", "time": 1777381504 }, "_maintainer": { "name": "António Sousa", "email": "aggode@utu.fi", "login": "antonioggsousa", "twitter": "@antonioggsousa", "description": "", "uuid": 22957109, "orcid": "0000-0003-4779-6459" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.2.0", "role": "Depends" }, { "package": "Matrix", "role": "Imports" }, { "package": "aricode", "role": "Imports" }, { "package": "LiblineaR", "role": "Imports" }, { "package": "SparseM", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "umap", "role": "Imports" }, { "package": "Rtsne", "role": "Imports" }, { "package": "pheatmap", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "RANN", "role": "Imports" }, { "package": "sparseMatrixStats", "role": "Imports" }, { "package": "irlba", "role": "Imports" }, { "package": "flexclust", "role": "Imports" }, { "package": "scran", "role": "Imports" }, { "package": "class", "role": "Imports" }, { "package": "matrixStats", "role": "Imports" }, { "package": "tidyr", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "uwot", "role": "Imports" }, { "package": "scatterpie", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "ggrastr", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "RSpectra", "role": "Imports" }, { "package": "BiocParallel", "role": "Imports" }, { "package": "withr", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "bluster", "role": "Suggests" }, { "package": "ComplexHeatmap", "role": "Suggests" }, { "package": "circlize", "role": "Suggests" }, { "package": "scater", "role": "Suggests" }, { "package": "viridis", "role": "Suggests" }, { "package": "scRNAseq", "role": "Suggests" }, { "package": "SingleR", "role": "Suggests" }, { "package": "MouseGastrulationData", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "scrapper", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-26", "n": 1 }, { "week": "2025-27", "n": 9 }, { "week": "2025-29", "n": 1 }, { "week": "2025-30", "n": 1 }, { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.3.0", "bioc": "3.24" }, { "branch": "release", "version": "1.2.0", "bioc": "3.23" } ], "_topics": [ "singlecell", "rnaseq", "proteomics", "transcriptomics", "geneexpression", "batcheffect", "clustering", "annotation", "classification", "differentialexpression", "dimensionreduction", "software", "data-integration", "scrna-seq" ], "_stars": 4, "_contributors": [ { "user": "antonioggsousa", "count": 58, "uuid": 22957109 }, { "user": "sinijun", "count": 1, "uuid": 123558824 }, { "user": "j0ntt", "count": 1, "uuid": 15635352 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 200, "source": "https://www.bioconductor.org/packages/stats/bioc/Coralysis" }, "_devurl": "https://github.com/elolab/coralysis", "_pkgdown": "https://elolab.github.io/Coralysis/", "_searchresults": 1, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/Coralysis.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/elolab/coralysis", "_realowner": "bioc", "_cranurl": false, "_exports": [ "AggregateDataByBatch", "BinCellClusterProbability", "CellBinsFeatureCorrelation", "CellClusterProbabilityDistribution", "FindAllClusterMarkers", "FindClusterMarkers", "GetCellClusterProbability", "GetFeatureCoefficients", "HeatmapFeatures", "MajorityVotingFeatures", "PCAElbowPlot", "PlotClusterTree", "PlotDimRed", "PlotExpression", "PrepareData", "ReferenceMapping", "RunParallelDivisiveICP", "RunPCA", "RunTSNE", "RunUMAP", "SummariseCellClusterProbability", "TabulateCellBinsByGroup", "VlnPlot" ], "_help": [ { "page": "AggregateDataByBatch", "title": "Aggregates feature expression by cell clusters, per batch if provided.", "topics": [ "AggregateDataByBatch", "AggregateDataByBatch,SingleCellExperiment-method", "AggregateDataByBatch.SingleCellExperiment" ] }, { "page": "BinCellClusterProbability", "title": "Bin cell cluster probability", "topics": [ "BinCellClusterProbability", "BinCellClusterProbability,SingleCellExperiment-method", "BinCellClusterProbability.SingleCellExperiment" ] }, { "page": "CellBinsFeatureCorrelation", "title": "Cell bins feature correlation", "topics": [ "CellBinsFeatureCorrelation", "CellBinsFeatureCorrelation,SingleCellExperiment-method", "CellBinsFeatureCorrelation.SingleCellExperiment" ] }, { "page": "CellClusterProbabilityDistribution", "title": "Cell cluster probability distribution", "topics": [ "CellClusterProbabilityDistribution", "CellClusterProbabilityDistribution,SingleCellExperiment-method", "CellClusterProbabilityDistribution.SingleCellExperiment" ] }, { "page": "FindAllClusterMarkers", "title": "Identification of feature markers for all clusters", "topics": [ "FindAllClusterMarkers", "FindAllClusterMarkers,SingleCellExperiment-method", "FindAllClusterMarkers.SingleCellExperiment" ] }, { "page": "FindClusterMarkers", "title": "Differential expression between cell clusters", "topics": [ "FindClusterMarkers", "FindClusterMarkers,SingleCellExperiment-method", "FindClusterMarkers.SingleCellExperiment" ] }, { "page": "GetCellClusterProbability", "title": "Get ICP cell cluster probability", "topics": [ "GetCellClusterProbability", "GetCellClusterProbability,SingleCellExperiment-method", "GetCellClusterProbability.SingleCellExperiment" ] }, { "page": "GetFeatureCoefficients", "title": "Get feature coefficients", "topics": [ "GetFeatureCoefficients", "GetFeatureCoefficients,SingleCellExperiment-method", "GetFeatureCoefficients.SingleCellExperiment" ] }, { "page": "HeatmapFeatures", "title": "Heatmap visualization of the expression of features by clusters", "topics": [ "HeatmapFeatures", "HeatmapFeatures,SingleCellExperiment-method", "HeatmapFeatures.SingleCellExperiment" ] }, { "page": "MajorityVotingFeatures", "title": "Majority voting features by label", "topics": [ "MajorityVotingFeatures", "MajorityVotingFeatures,SingleCellExperiment-method", "MajorityVotingFeatures.SingleCellExperiment" ] }, { "page": "PCAElbowPlot", "title": "Elbow plot of the standard deviations of the principal components", "topics": [ "PCAElbowPlot", "PCAElbowPlot,SingleCellExperiment-method", "PCAElbowPlot.SingleCellExperiment" ] }, { "page": "PlotClusterTree", "title": "Plot cluster tree", "topics": [ "PlotClusterTree", "PlotClusterTree,SingleCellExperiment-method", "PlotClusterTree.SingleCellExperiment" ] }, { "page": "PlotDimRed", "title": "Plot dimensional reduction categorical variables", "topics": [ "PlotDimRed", "PlotDimRed,SingleCellExperiment-method", "PlotDimRed.SingleCellExperiment" ] }, { "page": "PlotExpression", "title": "Plot dimensional reduction feature expression", "topics": [ "PlotExpression", "PlotExpression,SingleCellExperiment-method", "PlotExpression.SingleCellExperiment" ] }, { "page": "PrepareData", "title": "Prepare 'SingleCellExperiment' object for analysis", "topics": [ "PrepareData", "PrepareData,SingleCellExperiment-method", "PrepareData.SingleCellExperiment" ] }, { "page": "ReferenceMapping", "title": "Reference mapping", "topics": [ "ReferenceMapping", "ReferenceMapping,SingleCellExperiment,SingleCellExperiment-method", "ReferenceMapping.SingleCellExperiment" ] }, { "page": "RunParallelDivisiveICP", "title": "Multi-level integration", "topics": [ "RunParallelDivisiveICP", "RunParallelDivisiveICP,SingleCellExperiment-method", "RunParallelDivisiveICP.SingleCellExperiment" ] }, { "page": "RunPCA", "title": "Principal Component Analysis", "topics": [ "RunPCA", "RunPCA,SingleCellExperiment-method", "RunPCA.SingleCellExperiment" ] }, { "page": "RunTSNE", "title": "Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding (t-SNE)", "topics": [ "RunTSNE", "RunTSNE,SingleCellExperiment-method", "RunTSNE.SingleCellExperiment" ] }, { "page": "RunUMAP", "title": "Uniform Manifold Approximation and Projection (UMAP)", "topics": [ "RunUMAP", "RunUMAP,SingleCellExperiment-method", "RunUMAP.SingleCellExperiment" ] }, { "page": "SummariseCellClusterProbability", "title": "Summarise ICP cell cluster probability", "topics": [ "SummariseCellClusterProbability", "SummariseCellClusterProbability,SingleCellExperiment-method", "SummariseCellClusterProbability.SingleCellExperiment" ] }, { "page": "TabulateCellBinsByGroup", "title": "Tabulate cell bins by group", "topics": [ "TabulateCellBinsByGroup", "TabulateCellBinsByGroup,SingleCellExperiment-method", "TabulateCellBinsByGroup.SingleCellExperiment" ] }, { "page": "VlnPlot", "title": "Visualization of feature expression using violin plots", "topics": [ "VlnPlot", "VlnPlot,SingleCellExperiment-method", "VlnPlot.SingleCellExperiment" ] } ], "_readme": "https://github.com/bioc/Coralysis/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "aricode", "askpass", "assorthead", "base64enc", "beachmat", "beeswarm", "BH", "Biobase", "BiocGenerics", "BiocNeighbors", "BiocParallel", "BiocSingular", "bluster", "Cairo", "class", "cli", "cluster", "codetools", "cowplot", "cpp11", "DelayedArray", "digest", "dplyr", "dqrng", "edgeR", "farver", "flexclust", "FNN", "formatR", "fs", "futile.logger", "futile.options", "generics", "GenomicRanges", "ggbeeswarm", "ggforce", "ggfun", "ggplot2", "ggrastr", "ggrepel", "glue", "gtable", "here", "igraph", "IRanges", "irlba", "isoband", "jsonlite", "labeling", "lambda.r", "lattice", "LiblineaR", "lifecycle", "limma", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "metapod", "modeltools", "openssl", "pheatmap", "pillar", "pkgconfig", "plyr", "png", "polyclip", "purrr", "R6", "ragg", "RANN", "rappdirs", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppEigen", "RcppProgress", "RcppTOML", "reshape2", "reticulate", "rlang", "rprojroot", "RSpectra", "rsvd", "Rtsne", "S4Arrays", "S4Vectors", "S7", "ScaledMatrix", "scales", "scatterpie", "scran", "scuttle", "Seqinfo", "SingleCellExperiment", "sitmo", "snow", "SparseArray", "SparseM", "sparseMatrixStats", "statmod", "stringi", "stringr", "SummarizedExperiment", "sys", "systemfonts", "textshaping", "tibble", "tidyr", "tidyselect", "tweenr", "umap", "utf8", "uwot", "vctrs", "vipor", "viridisLite", "withr", "XVector", "yulab.utils" ], "_vignettes": [ { "source": "CellState.Rmd", "filename": "CellState.html", "title": "Cell states", "engine": "knitr::rmarkdown", "headings": [ "Dataset", "Normalization", "HVG selection", "Multi-level integration", "Dimensional reduction", "Cell state identification", "ICP clusters", "Graph-based clustering", "Cell cluster probability bins", "Differential expression programs", "R session", "References" ], "created": "2025-02-14 14:54:35", "modified": "2025-04-10 15:11:01", "commits": 8 }, { "source": "Coralysis.Rmd", "filename": "Coralysis.html", "title": "Coralysis: sensitive integration of single-cell data", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Installation", "Dataset", "Preprocess", "Multi-level integration", "Integrated embedding", "Nonlinear dimensional reduction", "Visualize batch & cell types", "Graph-based clustering", "Gene coefficients", "R session", "References" ], "created": "2025-02-13 15:50:09", "modified": "2025-04-10 15:11:01", "commits": 6 }, { "source": "Integration.Rmd", "filename": "Integration.html", "title": "Integration", "engine": "knitr::rmarkdown", "headings": [ "Dataset", "Normalization", "HVG selection", "DimRed: pre-integration", "Multi-level integration", "DimRed: post-integration", "Clustering", "Cluster markers", "DGE", "R session", "References" ], "created": "2025-02-14 14:42:12", "modified": "2025-04-10 15:11:01", "commits": 6 }, { "source": "RefMap.Rmd", "filename": "RefMap.html", "title": "Reference-mapping", "engine": "knitr::rmarkdown", "headings": [ "Dataset", "Train reference", "Map query", "Prediction accuracy", "Confusion matrix", "DimRed", "R session", "References" ], "created": "2025-02-14 14:42:12", "modified": "2025-07-17 13:21:15", "commits": 6 } ], "_score": 5.982271233039569, "_indexed": false, "_nocasepkg": "coralysis", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/Coralysis", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.2.0", "date": "2026-05-30T09:24:40.000Z", "distro": "noble", "commit": "24c1814b73cad37b5e240754cc5c650e743e69fd", "fileid": "f2239e35433ddd464fa96d3faa99e7a047aeadb48b50bcc8b51e84c7cff94d9b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679830194" }, { "r": "4.6.0", "os": "linux", "version": "1.2.0", "date": "2026-05-30T09:24:18.000Z", "distro": "noble", "commit": "24c1814b73cad37b5e240754cc5c650e743e69fd", "fileid": "435dfc7abd061bb38ca552e17149845723f6521225b48bccea88e8559166b26b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679830194" }, { "r": "4.5.3", "os": "mac", "version": "1.2.0", "date": "2026-05-30T12:52:31.000Z", "commit": "24c1814b73cad37b5e240754cc5c650e743e69fd", "fileid": "c04829b5a89fa82b92343a7a2702696bed39448521027811ac10bc8909ad20e1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679830194" }, { "r": "4.6.0", "os": "mac", "version": "1.2.0", "date": "2026-05-30T12:51:12.000Z", "commit": "24c1814b73cad37b5e240754cc5c650e743e69fd", "fileid": "eb7fc92faf86997c889091a64a68838036841cfd6426fe0359f0be2c68eecbd3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679830194" }, { "r": "4.6.0", "os": "wasm", "version": "1.2.0", "date": "2026-05-30T09:23:17.000Z", "commit": "24c1814b73cad37b5e240754cc5c650e743e69fd", "fileid": "8c7c84d5497012ff55b4198387bb87de52f37c4639271cd4a5c1bf93eedd6441", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679830194" }, { "r": "4.7.0", "os": "win", "version": "1.2.0", "date": "2026-05-30T09:39:11.000Z", "commit": "24c1814b73cad37b5e240754cc5c650e743e69fd", "fileid": "c0e5a4c226d8c97d2e0ef515ef402ae28424b14679d6339aae1d148732746e03", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679830194" }, { "r": "4.5.3", "os": "win", "version": "1.2.0", "date": "2026-05-30T09:38:36.000Z", "commit": "24c1814b73cad37b5e240754cc5c650e743e69fd", "fileid": "0f39a9a60679d2234910b72b1a00b20ada97d210def5e87bb6cebf8600939ac0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679830194" }, { "r": "4.6.0", "os": "win", "version": "1.2.0", "date": "2026-05-30T09:38:49.000Z", "commit": "24c1814b73cad37b5e240754cc5c650e743e69fd", "fileid": "ca7cbfc39ee4f8571c9fd0daa4546ec8e65f705ccdd0aa4c82fe1aee1bfe8fda", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26679830194" } ] }