{ "_id": "6a101babacfb0bcc41c8752b", "Type": "Package", "Package": "SCpubr", "Title": "Generate Publication Ready Visualizations of Single Cell\nTranscriptomics Data", "Version": "3.0.1", "Authors@R": "person(\"Enrique\", \"Blanco-Carmona\", , \"scpubr@gmail.com\", role = c(\"cre\", \"aut\"),\ncomment = c(ORCID = \"0000-0002-1208-1691\"))", "Description": "A system that provides a streamlined way of generating\npublication ready plots for known Single-Cell transcriptomics\ndata in a “publication ready” format. This is, the goal is to\nautomatically generate plots with the highest quality possible,\nthat can be used right away or with minimal modifications for a\nresearch article.", "License": "GPL-3", "URL": "https://github.com/enblacar/SCpubr/,\nhttps://enblacar.github.io/SCpubr-book/", "BugReports": "https://github.com/enblacar/SCpubr/issues/", "VignetteBuilder": "knitr", "biocViews": "Software, SingleCell, Visualization", "Config/testthat/edition": "3", "Encoding": "UTF-8", "LazyData": "true", "LazyDataCompression": "xz", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Repository": "https://enblacar.r-universe.dev", "Date/Publication": "2026-03-02 09:25:10 UTC", "RemoteUrl": "https://github.com/enblacar/scpubr", "RemoteRef": "HEAD", "RemoteSha": "a3ae2999ce50f32b96a68664f1880faafe94f01e", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-14 09:03:24 UTC", "User": "root" }, "Author": "Enrique Blanco-Carmona [cre, aut] (ORCID:\n)", "Maintainer": "Enrique Blanco-Carmona ", "MD5sum": "96a53fbd4db0f8581226c237c26ba523", "_user": "enblacar", "_type": "src", "_file": "SCpubr_3.0.1.tar.gz", "_fileid": "14b6db7d9fd083472a49dd0cbafe4849419e5e62a3cc382b961559074ab38bc3", "_filesize": 2024690, "_sha256": "14b6db7d9fd083472a49dd0cbafe4849419e5e62a3cc382b961559074ab38bc3", "_created": "2026-05-14T09:03:24.000Z", "_published": "2026-05-22T09:02:35.019Z", "_distro": "noble", "_jobs": [ { "job": 77348505674, "time": 289, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "6990986481" }, { "job": 77348505527, "time": 308, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "6990994043" }, { "job": 77348506015, "time": 208, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "6990956515" }, { "job": 77348505276, "time": 232, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "6990961292" }, { "job": 77348504792, "time": 310, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6990901772" }, { "job": 77348505056, "time": 218, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7156768005" }, { "job": 77348505291, "time": 577, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "6991070478" }, { "job": 77348505748, "time": 462, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "6991037222" }, { "job": 77348506090, "time": 470, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "6991039760" } ], "_buildurl": "https://github.com/r-universe/enblacar/actions/runs/25851334066", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/enblacar/scpubr", "_commit": { "id": "a3ae2999ce50f32b96a68664f1880faafe94f01e", "author": "enblacar ", "committer": "enblacar ", "message": "Fixed bug in DotPlot not accessing metadata columns.\n", "time": 1772443510 }, "_maintainer": { "name": "Enrique Blanco-Carmona", "email": "scpubr@gmail.com", "login": "enblacar", "orcid": "0000-0002-1208-1691", "twitter": "@Enblacar", "uuid": 42321264 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "assertthat", "role": "Suggests" }, { "package": "circlize", "role": "Suggests" }, { "package": "cli", "role": "Suggests" }, { "package": "cluster", "role": "Suggests" }, { "package": "colorspace", "role": "Suggests" }, { "package": "ComplexHeatmap", "role": "Suggests" }, { "package": "covr", "role": "Suggests" }, { "package": "decoupleR", "role": "Suggests" }, { "package": "dplyr", "version": ">= 1.1.0", "role": "Suggests" }, { "package": "enrichplot", "role": "Suggests" }, { "package": "forcats", "role": "Suggests" }, { "package": "ggalluvial", "version": ">= 0.12.5", "role": "Suggests" }, { "package": "ggbeeswarm", "role": "Suggests" }, { "package": "ggdist", "role": "Suggests" }, { "package": "ggExtra", "role": "Suggests" }, { "package": "ggh4x", "role": "Suggests" }, { "package": "ggplot2", "version": ">= 3.4.0", "role": "Suggests" }, { "package": "ggplotify", "role": "Suggests" }, { "package": "ggrastr", "role": "Suggests" }, { "package": "ggrepel", "role": "Suggests" }, { "package": "ggridges", "role": "Suggests" }, { "package": "ggsignif", "role": "Suggests" }, { "package": "graphics", "role": "Suggests" }, { "package": "infercnv", "role": "Suggests" }, { "package": "KernSmooth", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "labeling", "role": "Suggests" }, { "package": "magrittr", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" }, { "package": "Matrix", "role": "Suggests" }, { "package": "methods", "role": "Suggests" }, { "package": "Nebulosa", "role": "Suggests" }, { "package": "org.Hs.eg.db", "role": "Suggests" }, { "package": "patchwork", "role": "Suggests" }, { "package": "pheatmap", "role": "Suggests" }, { "package": "plyr", "role": "Suggests" }, { "package": "purrr", "role": "Suggests" }, { "package": "qpdf", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "rjags", "role": "Suggests" }, { "package": "rlang", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "scales", "role": "Suggests" }, { "package": "scattermore", "role": "Suggests" }, { "package": "Seurat", "role": "Suggests" }, { "package": "SeuratObject", "role": "Suggests" }, { "package": "sf", "role": "Suggests" }, { "package": "stringr", "role": "Suggests" }, { "package": "svglite", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "tidyr", "role": "Suggests" }, { "package": "UCell", "role": "Suggests" }, { "package": "viridis", "role": "Suggests" }, { "package": "withr", "role": "Suggests" } ], "_owner": "enblacar", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-21", "n": 1 }, { "week": "2025-29", "n": 4 }, { "week": "2025-30", "n": 3 }, { "week": "2025-32", "n": 2 }, { "week": "2025-52", "n": 1 }, { "week": "2026-09", "n": 2 }, { "week": "2026-10", "n": 1 } ], "_tags": [], "_topics": [ "software", "singlecell", "visualization", "data-visualization", "ggplot2", "publication-quality-plots", "seurat", "single-cell", "single-cell-genomics", "single-cell-rna-seq" ], "_stars": 222, "_contributors": [ { "user": "enblacar", "count": 753, "uuid": 42321264 }, { "user": "nbpeterson3", "count": 7, "uuid": 68209187 }, { "user": "mojaveazure", "count": 1, "uuid": 11035068 }, { "user": "safwat08", "count": 1, "uuid": 55861735 } ], "_userbio": { "uuid": 42321264, "type": "user", "name": "Enrique Blanco Carmona", "description": "Bioinformatics Data Scientist" }, "_downloads": { "count": 1006, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SCpubr" }, "_devurl": "https://github.com/enblacar/scpubr", "_searchresults": 387, "_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/SCpubr.html", "manual.pdf" ], "_homeurl": "https://github.com/enblacar/scpubr", "_realowner": "enblacar", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2022-10-14" }, { "version": "1.0.1", "date": "2022-10-17" }, { "version": "1.0.2", "date": "2022-10-25" }, { "version": "1.0.3", "date": "2022-11-07" }, { "version": "1.0.4", "date": "2022-11-07" }, { "version": "1.1.0", "date": "2023-01-14" }, { "version": "1.1.1", "date": "2023-01-14" }, { "version": "1.1.2", "date": "2023-01-18" }, { "version": "2.0.0", "date": "2023-08-10" }, { "version": "2.0.1", "date": "2023-08-13" }, { "version": "2.0.2", "date": "2023-10-11" }, { "version": "3.0.0", "date": "2025-08-20" }, { "version": "3.0.1", "date": "2026-01-09" } ], "_exports": [ "do_ActivityHeatmap", "do_AlluvialPlot", "do_BarPlot", "do_BeeSwarmPlot", "do_BoxPlot", "do_CellularStatesPlot", "do_ChordDiagramPlot", "do_CNVHeatmap", "do_ColorBlindCheck", "do_ColorPalette", "do_CorrelationHeatmap", "do_DimPlot", "do_DotPlot", "do_EnrichmentHeatmap", "do_ExpressionHeatmap", "do_FeaturePlot", "do_GroupwiseDEHeatmap", "do_LigandReceptorPlot", "do_LoadingsHeatmap", "do_MetadataHeatmap", "do_NebulosaPlot", "do_PackageReport", "do_PathwayActivityHeatmap", "do_RankedEnrichmentHeatmap", "do_RankedExpressionHeatmap", "do_RidgePlot", "do_SCEnrichmentHeatmap", "do_SCExpressionHeatmap", "do_StripPlot", "do_TermEnrichmentPlot", "do_TFActivityHeatmap", "do_ViolinPlot", "do_VolcanoPlot", "do_WafflePlot" ], "_datasets": [ { "name": "human_chr_locations", "title": "Chromosome arm locations for human genome GRCh38.", "object": "human_chr_locations", "class": [ "tbl_df", "tbl", "data.frame" ], "fields": [ "chr", "arm", "start", "end" ], "rows": 48, "table": true, "tojson": true } ], "_help": [ { "page": "do_ActivityHeatmap", "title": "Compute affinity of gene sets to cell populations using decoupleR.", "topics": [ "do_ActivityHeatmap" ] }, { "page": "do_AlluvialPlot", "title": "Generate Alluvial plots.", "topics": [ "do_AlluvialPlot" ] }, { "page": "do_BarPlot", "title": "Create Bar Plots.", "topics": [ "do_BarPlot" ] }, { "page": "do_BeeSwarmPlot", "title": "Generate BeeSwarm plots of ranked cells colored by gene expression or metadata.", "topics": [ "do_BeeSwarmPlot" ] }, { "page": "do_BoxPlot", "title": "Generate Box Plots.", "topics": [ "do_BoxPlot" ] }, { "page": "do_CellularStatesPlot", "title": "Plot relationships between enrichment scores to infer cellular states.", "topics": [ "do_CellularStatesPlot" ] }, { "page": "do_ChordDiagramPlot", "title": "Generate a Chord diagram.", "topics": [ "do_ChordDiagramPlot" ] }, { "page": "do_CNVHeatmap", "title": "Display CNV scores from inferCNV as Feature Plots.", "topics": [ "do_CNVHeatmap" ] }, { "page": "do_ColorBlindCheck", "title": "Generate colorblind variations of a given color palette.", "topics": [ "do_ColorBlindCheck" ] }, { "page": "do_ColorPalette", "title": "Generate color scales based on a value.", "topics": [ "do_ColorPalette" ] }, { "page": "do_CorrelationHeatmap", "title": "Create correlation matrix heatmaps.", "topics": [ "do_CorrelationHeatmap" ] }, { "page": "do_DimPlot", "title": "Generate dimensional reduction plots from a Seurat object.", "topics": [ "do_DimPlot" ] }, { "page": "do_DotPlot", "title": "Generate Dot plots of gene expression across cell groups.", "topics": [ "do_DotPlot" ] }, { "page": "do_EnrichmentHeatmap", "title": "Create enrichment scores heatmaps.", "topics": [ "do_EnrichmentHeatmap" ] }, { "page": "do_ExpressionHeatmap", "title": "Create heatmaps of averaged expression by groups.", "topics": [ "do_ExpressionHeatmap" ] }, { "page": "do_FeaturePlot", "title": "Plot gene expression on dimensional reduction embeddings.", "topics": [ "do_FeaturePlot" ] }, { "page": "do_GroupwiseDEHeatmap", "title": "Compute a dotplot with the results of a group-wise DE analysis.", "topics": [ "do_GroupwiseDEHeatmap" ] }, { "page": "do_LigandReceptorPlot", "title": "Visualize Ligand-Receptor analysis output.", "topics": [ "do_LigandReceptorPlot" ] }, { "page": "do_LoadingsHeatmap", "title": "Compute a heatmap summary of the top and bottom genes in the PCA loadings for the desired PCs in a Seurat object.", "topics": [ "do_LoadingsHeatmap" ] }, { "page": "do_MetadataHeatmap", "title": "Compute a heatmap of categorical variables.", "topics": [ "do_MetadataHeatmap" ] }, { "page": "do_NebulosaPlot", "title": "Plot kernel density estimates of gene expression on dimensional reduction embeddings.", "topics": [ "do_NebulosaPlot" ] }, { "page": "do_PackageReport", "title": "Generate a status report of SCpubr and its dependencies.", "topics": [ "do_PackageReport" ] }, { "page": "do_PathwayActivityHeatmap", "title": "Plot Pathway Activities from decoupleR using Progeny prior knowledge.", "topics": [ "do_PathwayActivityHeatmap" ] }, { "page": "do_RankedEnrichmentHeatmap", "title": "Compute a heatmap of enrichment of gene sets on the context of a dimensional reduction component.", "topics": [ "do_RankedEnrichmentHeatmap" ] }, { "page": "do_RankedExpressionHeatmap", "title": "Compute a heatmap of expression of genes on the context of a dimensional reduction component.", "topics": [ "do_RankedExpressionHeatmap" ] }, { "page": "do_RidgePlot", "title": "Create ridge plots.", "topics": [ "do_RidgePlot" ] }, { "page": "do_SCEnrichmentHeatmap", "title": "Perform a single-cell-based heatmap showing the enrichment in a list of gene sets.", "topics": [ "do_SCEnrichmentHeatmap" ] }, { "page": "do_SCExpressionHeatmap", "title": "Perform a single-cell-based heatmap showing the expression of genes.", "topics": [ "do_SCExpressionHeatmap" ] }, { "page": "do_StripPlot", "title": "Generate a Strip plot.", "topics": [ "do_StripPlot" ] }, { "page": "do_TermEnrichmentPlot", "title": "Display the enriched terms for a given list of genes.", "topics": [ "do_TermEnrichmentPlot" ] }, { "page": "do_TFActivityHeatmap", "title": "Plot TF Activities from decoupleR using Dorothea prior knowledge.", "topics": [ "do_TFActivityHeatmap" ] }, { "page": "do_ViolinPlot", "title": "Generate Violin plots from a Seurat object.", "topics": [ "do_ViolinPlot" ] }, { "page": "do_VolcanoPlot", "title": "Compute a Volcano plot out of DE genes.", "topics": [ "do_VolcanoPlot" ] }, { "page": "do_WafflePlot", "title": "Generate Waffle plots to display cell group proportions.", "topics": [ "do_WafflePlot" ] }, { "page": "human_chr_locations", "title": "Chromosome arm locations for human genome GRCh38.", "topics": [ "human_chr_locations" ] } ], "_pkglogo": "https://github.com/enblacar/scpubr/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/enblacar/scpubr/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "reference_manual.Rmd", "filename": "reference_manual.html", "title": "reference_manual", "engine": "knitr::rmarkdown", "headings": [], "created": "2022-10-10 12:44:52", "modified": "2023-07-31 11:12:19", "commits": 2 } ], "_score": 9.434972473979059, "_indexed": true, "_nocasepkg": "scpubr", "_universes": [ "enblacar" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.0.1", "date": "2026-05-14T09:07:21.000Z", "distro": "noble", "commit": "a3ae2999ce50f32b96a68664f1880faafe94f01e", "fileid": "7595e1d52fea676facafdff7f37d3fe58cc09312bd073db949b665c4c447e1c9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/enblacar/actions/runs/25851334066" }, { "r": "4.6.0", "os": "linux", "version": "3.0.1", "date": "2026-05-14T09:07:44.000Z", "distro": "noble", "commit": "a3ae2999ce50f32b96a68664f1880faafe94f01e", "fileid": "f17eb9535196c06a24e428b433dd515a804cde8984f6c8146da7a150ef188416", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/enblacar/actions/runs/25851334066" }, { "r": "4.5.3", "os": "mac", "version": "3.0.1", "date": "2026-05-14T09:06:10.000Z", "commit": "a3ae2999ce50f32b96a68664f1880faafe94f01e", "fileid": "716ec63030c378cc0166c9b18ec91696756272eb53ea9c6eb265a7144f4a5c79", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/enblacar/actions/runs/25851334066" }, { "r": "4.6.0", "os": "mac", "version": "3.0.1", "date": "2026-05-14T09:06:19.000Z", "commit": "a3ae2999ce50f32b96a68664f1880faafe94f01e", "fileid": "557871af2e98b1118e6faba8cf3b9d0c1dd191b51aaae3155b95fb1d2b51a455", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/enblacar/actions/runs/25851334066" }, { "r": "4.7.0", "os": "win", "version": "3.0.1", "date": "2026-05-14T09:11:37.000Z", "commit": "a3ae2999ce50f32b96a68664f1880faafe94f01e", "fileid": "d60a6a7facef5f9334f1a2fe7f6ca5728aff8e8dda4368c0ba409f9f0399e87e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/enblacar/actions/runs/25851334066" }, { "r": "4.5.3", "os": "win", "version": "3.0.1", "date": "2026-05-14T09:09:57.000Z", "commit": "a3ae2999ce50f32b96a68664f1880faafe94f01e", "fileid": "49bbe4a9767044c0d18f7e414f80f646e2104929280b9afc68958f588b274118", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/enblacar/actions/runs/25851334066" }, { "r": "4.6.0", "os": "win", "version": "3.0.1", "date": "2026-05-14T09:10:00.000Z", "commit": "a3ae2999ce50f32b96a68664f1880faafe94f01e", "fileid": "83306c768dd49a3fd9bd27940b725d08094bcc1dd58720dad75e4ddefe2ca527", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/enblacar/actions/runs/25851334066" }, { "r": "4.6.0", "os": "wasm", "version": "3.0.1", "date": "2026-05-22T09:02:10.000Z", "commit": "a3ae2999ce50f32b96a68664f1880faafe94f01e", "fileid": "073680e000637e29ac7d6988f216e5584fdbe1af3fbe584cd58cea23493c059d", "status": "success", "buildurl": "https://github.com/r-universe/enblacar/actions/runs/25851334066" } ] }