{ "_id": "6ac74f46de46216d5edce31a", "Package": "scGenePanel", "Title": "Multi-panel visualization for single cell expression data", "Version": "0.99.0", "Authors@R": "c(\nperson(\ngiven = \"Shristi\",\nfamily = \"Shrestha\",\nemail = \"shristi.shrestha.2@vanderbilt.edu\",\nrole = c(\"aut\"),\ncomment = c(ORCID = \"0000-0003-4519-1712\")),\nperson(\ngiven = \"Jean-Philippe\",\nfamily = \"Cartailler\",\nemail = \"jp.cartailler@vanderbilt.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-0312-2391\"))\n)", "License": "AGPL-3 + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.2", "Description": "scGenePanel creates coordinated, gene-centric multi-panel\nvisualizations for single-cell RNA-seq data stored in Seurat or\nSingleCellExperiment objects. It combines group-stratified UMAP\nembeddings, cell-type-specific expression distributions, and\nquantitative cell-frequency and expression summaries in a\nsingle figure. An accompanying Shiny application supports\ninteractive exploration using the same workflow.", "biocViews": "Software, GeneExpression, SingleCell, Visualization,\nDimensionReduction, Transcriptomics", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "BugReports": "https://github.com/vandydata/scGenePanel/issues", "URL": "https://github.com/vandydata/scGenePanel", "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://biocstaging.r-universe.dev", "Date/Publication": "2026-09-08 01:06:56 UTC", "RemoteUrl": "https://github.com/BiocStaging/scGenePanel", "RemoteRef": "HEAD", "RemoteSha": "172d0bd70d73bbdc0508573f8a93c2ad61247520", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-08 07:59:42 UTC", "User": "root" }, "Author": "Shristi Shrestha [aut] (ORCID: ),\nJean-Philippe Cartailler [aut, cre] (ORCID:\n)", "Maintainer": "Jean-Philippe Cartailler ", "_user": "biocstaging", "_type": "src", "_file": "scGenePanel_0.99.0.tar.gz", "_fileid": "https://r2.ropensci.org/88133bf488a67a799c21e286ca0584f6ff97c7ed54b6578d17a53fc9d4e2e259", "_filesize": 7901221, "_sha256": "88133bf488a67a799c21e286ca0584f6ff97c7ed54b6578d17a53fc9d4e2e259", "_expires": "2027-01-16T08:07:31.000Z", "_created": "2026-10-08T07:59:42.000Z", "_published": "2026-10-08T08:07:33.930Z", "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37746357798", "_status": "success", "_host": "GitHub-Actions", "_bioccheck": { "error": 0, "warning": 0, "note": 4 }, "_upstream": "https://github.com/BiocStaging/scGenePanel", "_commit": { "id": "172d0bd70d73bbdc0508573f8a93c2ad61247520", "author": "JP Cartailler ", "committer": "JP Cartailler ", "message": "Remove development files from Bioconductor submission branch\n", "time": 1788829616 }, "_maintainer": { "name": "Jean-Philippe Cartailler", "email": "jp.cartailler@vanderbilt.edu", "login": "jpcartailler", "description": "", "uuid": 5258731, "orcid": "0000-0002-0312-2391" }, "_distro": "resolute", "_jobs": [ { "job": 113210755488, "time": 249, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "11536172339" }, { "job": 113210755571, "time": 315, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11536087621" }, { "job": 113210755552, "time": 402, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11535944999" }, { "job": 113210755546, "time": 248, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11535729720" }, { "job": 113210755557, "time": 242, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11536626181" }, { "job": 113208758295, "time": 348, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11536372196" }, { "job": 113210755514, "time": 196, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11536615744" }, { "job": 113210755605, "time": 344, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11537005195" }, { "job": 113210755618, "time": 298, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11536855515" }, { "job": 113210755634, "time": 373, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11536069411" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "Seurat", "version": ">= 4.1.1", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "dplyr", "role": "Imports" }, { "package": "magrittr", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggpubr", "role": "Imports" }, { "package": "ggforce", "role": "Imports" }, { "package": "ggthemes", "role": "Imports" }, { "package": "ggsci", "role": "Imports" }, { "package": "cowplot", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "grid", "role": "Imports" }, { "package": "gridExtra", "role": "Imports" }, { "package": "flextable", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "scCustomize", "role": "Imports" }, { "package": "shiny", "role": "Imports" }, { "package": "shinydashboard", "role": "Imports" }, { "package": "shinyjs", "role": "Imports" }, { "package": "shinyWidgets", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocManager", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" } ], "_owner": "biocstaging", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-37", "n": 2 } ], "_tags": [], "_topics": [ "software", "geneexpression", "singlecell", "visualization", "dimensionreduction", "transcriptomics" ], "_stars": 0, "_contributors": [ { "user": "jpcartailler", "count": 106, "uuid": 5258731 }, { "user": "shristi-shrestha", "count": 5, "uuid": 10420779 }, { "user": "c5creative", "count": 1, "uuid": 155905582 } ], "_userbio": { "uuid": 278472782, "type": "organization", "name": "BiocStaging", "followers": 2 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/scGenePanel" }, "_devurl": "https://github.com/vandydata/scgenepanel", "_searchresults": 2, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/scGenePanel.html", "LICENSE" ], "_cranurl": false, "_exports": [ "scGenePanel", "scGenePanelShiny" ], "_help": [ { "page": "dot-check_if_dim_red_exists", "title": "Check if dimension reduction embedding exists", "topics": [ ".check_if_dim_red_exists" ] }, { "page": "discrete_col_palette", "title": "Discrete color palettes from multiple packages (varibow, Rcolorbrewer, ggtheme)", "topics": [ "discrete_col_palette" ] }, { "page": "scgenepanel", "title": "scGenePanel - A method for generating scRNAseq multi-panel gene expression visuals that are focused on one gene, all cell types, and a chosen metadata attribute of interest.", "topics": [ "scGenePanel" ] }, { "page": "scGenePanelShiny", "title": "Launch Interactive Gene Panel Shiny Application", "topics": [ "scGenePanelShiny" ] } ], "_readme": "https://github.com/BiocStaging/scGenePanel/raw/HEAD/README.md", "_rundeps": [ "abind", "askpass", "backports", "base64enc", "beeswarm", "BH", "Biobase", "BiocGenerics", "bitops", "boot", "broom", "bslib", "cachem", "Cairo", "car", "carData", "caTools", "circlize", "cli", "cluster", "codetools", "colorspace", "commonmark", "corrplot", "cowplot", "cpp11", "crosstalk", "curl", "data.table", "DelayedArray", "deldir", "Deriv", "digest", "doBy", "dotCall64", "dplyr", "dqrng", "evaluate", "farver", "fastDummies", "fastmap", "fitdistrplus", "flextable", "FNN", "fontawesome", "fontBitstreamVera", "fontLiberation", "fontquiver", "forcats", "forecast", "Formula", "fracdiff", "fs", "future", "future.apply", "gdtools", "generics", "GenomicRanges", "ggbeeswarm", "ggforce", "ggplot2", "ggprism", "ggpubr", "ggrastr", "ggrepel", "ggridges", "ggsci", "ggsignif", "ggthemes", "GlobalOptions", "globals", "glue", "goftest", "gplots", "gridExtra", "gtable", "gtools", "here", "highr", "hms", "htmltools", "htmlwidgets", "httpuv", "httr", "ica", "igraph", "IRanges", "irlba", "isoband", "janitor", "jquerylib", "jsonlite", "KernSmooth", "knitr", "labeling", "later", "lattice", "lazyeval", "lifecycle", "listenv", "lme4", "lmtest", "lubridate", "magrittr", "MASS", "Matrix", "MatrixGenerics", "MatrixModels", "matrixStats", "mcprogress", "memoise", "mgcv", "mime", "miniUI", "minqa", "modelr", "nlme", "nloptr", "nnet", "numDeriv", "officer", "openssl", "otel", "paletteer", "parallelly", "patchwork", "pbapply", "pbkrtest", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "polynom", "prismatic", "progressr", "promises", "purrr", "quantreg", "R6", "ragg", "RANN", "rappdirs", "rbibutils", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppHNSW", "RcppProgress", "RcppThread", "RcppTOML", "Rdpack", "reformulas", "rematch2", "reshape2", "reticulate", "rlang", "rmarkdown", "ROCR", "rprojroot", "RSpectra", "rstatix", "rstudioapi", "Rtsne", "S4Arrays", "S4Vectors", "S7", "sass", "scales", "scattermore", "scCustomize", "sctransform", "Seqinfo", "Seurat", "SeuratObject", "shape", "shiny", "shinydashboard", "shinyjs", "shinyWidgets", "SingleCellExperiment", "sitmo", "snakecase", "sourcetools", "sp", "spam", "SparseArray", "SparseM", "spatstat.data", "spatstat.explore", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "systemfonts", "tensor", "textshaping", "tibble", "tidyr", "tidyselect", "timechange", "timeDate", "tinytex", "tweenr", "urca", "utf8", "uuid", "uwot", "vctrs", "vipor", "viridisLite", "withr", "xfun", "xml2", "xtable", "XVector", "yaml", "zip", "zoo" ], "_vignettes": [ { "source": "scGenePanel.Rmd", "filename": "scGenePanel.html", "title": "Getting Started with scGenePanel", "author": "Shristi Shrestha, Jean-Philippe Cartailler", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Why scGenePanel in Bioconductor?", "Features of scGenePanel visual", "Installation", "Data included in this package", "Load data", "Create a multi-panel plot", "Session information" ], "created": "2023-07-22 01:13:26", "modified": "2026-09-08 01:00:22", "commits": 6 } ], "_score": 3, "_indexed": true, "_nocasepkg": "scgenepanel", "_universes": [ "biocstaging", "jpcartailler", "vandydata" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.0", "date": "2026-10-08T08:03:00.000Z", "distro": "resolute", "commit": "172d0bd70d73bbdc0508573f8a93c2ad61247520", "fileid": "https://r2.ropensci.org/50748f1b1bbf80a35132451ca0212820244e5fe5e26673aeb25e667c6ee4111e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37746357798" }, { "r": "4.6.1", "os": "linux", "version": "0.99.0", "date": "2026-10-08T08:03:36.000Z", "distro": "resolute", "commit": "172d0bd70d73bbdc0508573f8a93c2ad61247520", "fileid": "https://r2.ropensci.org/abaf7b2ab9177e0e01fab0c37dfcbedb2bc08b1ccf159504acebed111fd68b0f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37746357798" }, { "r": "4.5.3", "os": "mac", "version": "0.99.0", "date": "2026-10-08T08:02:02.000Z", "commit": "172d0bd70d73bbdc0508573f8a93c2ad61247520", "fileid": "https://r2.ropensci.org/0df5b1507e8e4e79f504ddcb9d62a577924e009caf41bf5117055551a10631b8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37746357798" }, { "r": "4.6.1", "os": "mac", "version": "0.99.0", "date": "2026-10-08T08:01:55.000Z", "commit": "172d0bd70d73bbdc0508573f8a93c2ad61247520", "fileid": "https://r2.ropensci.org/0372641b20172742b81d49f77cf8ec0bc1623a719baefbff14d2017de84e9e78", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37746357798" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.0", "date": "2026-10-08T08:03:39.000Z", "commit": "172d0bd70d73bbdc0508573f8a93c2ad61247520", "fileid": "https://r2.ropensci.org/71ef1002c4abdcb3ce7b60e61cde0aac9693a3741cef4365d1728a14cf925323", "status": "success", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37746357798" }, { "r": "4.7.0", "os": "win", "version": "0.99.0", "date": "2026-10-08T08:01:53.000Z", "commit": "172d0bd70d73bbdc0508573f8a93c2ad61247520", "fileid": "https://r2.ropensci.org/e44d4891cd5829dbcabcf5124e93a9b08d658bb3708786433d3c126815ece4eb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37746357798" }, { "r": "4.5.3", "os": "win", "version": "0.99.0", "date": "2026-10-08T08:01:51.000Z", "commit": "172d0bd70d73bbdc0508573f8a93c2ad61247520", "fileid": "https://r2.ropensci.org/843a7b153812187138a9f826bd253cbee5762d006bfd1e45752184a4869cf792", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37746357798" }, { "r": "4.6.1", "os": "win", "version": "0.99.0", "date": "2026-10-08T08:02:44.000Z", "commit": "172d0bd70d73bbdc0508573f8a93c2ad61247520", "fileid": "https://r2.ropensci.org/16e441322dcdce3ca620cbc5bbb7d19a4f7af95ce8f1baa3561a13bdf7fcac25", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/37746357798" } ] }