{ "_id": "6a1b02171d7bb097a0a00a20", "Package": "scTreeViz", "Type": "Package", "Title": "R/Bioconductor package to interactively explore and visualize\nsingle cell RNA-seq datasets with hierarhical annotations", "Version": "1.19.0", "Authors@R": "c( \nperson(\"Jayaram\", \"Kancherla\", email=\"jayaram.kancherla@gmail.com\", role=c(\"aut\", \"cre\")),\nperson(\"Hector\", \"Corrada Bravo\", email=\"hcorrada@gmail.com\", role=c(\"aut\")),\nperson(\"Kazi Tasnim\", \"Zinat\", email=\"kzintas@umd.edu\", role=c(\"aut\")),\nperson(\"Stephanie\", \"Hicks\", email=\"shicks19@jhu.edu\", role=c(\"aut\"))\n)", "Description": "scTreeViz provides classes to support interactive data\naggregation and visualization of single cell RNA-seq datasets\nwith hierarchies for e.g. cell clusters at different\nresolutions. The `TreeIndex` class provides methods to manage\nhierarchy and split the tree at a given resolution or across\nresolutions. The `TreeViz` class extends `SummarizedExperiment`\nand can performs quick aggregations on the count matrix defined\nby clusters.", "License": "Artistic-2.0", "VignetteBuilder": "knitr", "biocViews": "Visualization, Infrastructure, GUI, SingleCell", "Encoding": "UTF-8", "Collate": "'TreeIndex-class.R' 'TreeIndex-methods.R' 'TreeViz-class.R'\n'TreeViz-methods.R' 'startTreeViz.R' 'TreeVizApp-class.R'\n'EpivizTreeData-class.R' 'helper-functions.R'\n'ClusterHierarchy-class.R'", "RoxygenNote": "7.1.1", "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libglpk-dev make\nlibharfbuzz-dev libbz2-dev libicu-dev libjpeg-dev liblzma-dev\nlibpng-dev libtiff-dev libuv1-dev libwebp-dev libxml2-dev\nlibssl-dev python3 xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:57:06 UTC", "RemoteUrl": "https://github.com/bioc/scTreeViz", "RemoteRef": "HEAD", "RemoteSha": "dd15f611114a451159c57445cab5d61496dbf137", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 09:55:02 UTC", "User": "root" }, "Author": "Jayaram Kancherla [aut, cre],\nHector Corrada Bravo [aut],\nKazi Tasnim Zinat [aut],\nStephanie Hicks [aut]", "Maintainer": "Jayaram Kancherla ", "MD5sum": "8613ef7e53a09a784c0db4eef6cde9d1", "_user": "bioc", "_type": "src", "_file": "scTreeViz_1.19.0.tar.gz", "_fileid": "f0eca9191081c596d15e7aee6a3bfafd178febc9ec73a252f585dd5a838595d0", "_filesize": 2318723, "_sha256": "f0eca9191081c596d15e7aee6a3bfafd178febc9ec73a252f585dd5a838595d0", "_created": "2026-05-30T09:55:02.000Z", "_published": "2026-05-30T15:28:23.092Z", "_jobs": [ { "job": 78641055536, "time": 353, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7307613835" }, { "job": 78641055534, "time": 668, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7307644009" }, { "job": 78641055529, "time": 683, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7307645513" }, { "job": 78641055557, "time": 331, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7309235682" }, { "job": 78641055537, "time": 436, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7309245253" }, { "job": 78639999623, "time": 535, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7307341427" }, { "job": 78641055523, "time": 273, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7307606163" }, { "job": 78641055556, "time": 1888, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7307756166" }, { "job": 78641055555, "time": 1719, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7307741247" }, { "job": 78641055551, "time": 1448, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7307715533" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 14 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26676994996", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/scTreeViz", "_commit": { "id": "dd15f611114a451159c57445cab5d61496dbf137", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381026 }, "_maintainer": { "name": "Jayaram Kancherla", "email": "jayaram.kancherla@gmail.com", "login": "jkanche", "bluesky": "@jkanche.bsky.social", "twitter": "@jayaram", "description": "Python, Genomics, JavaScript & everything in between.", "uuid": 399324 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "methods", "role": "Depends" }, { "package": "epivizr", "role": "Depends" }, { "package": "SummarizedExperiment", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "S4Vectors", "role": "Imports" }, { "package": "digest", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "Rtsne", "role": "Imports" }, { "package": "httr", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "clustree", "role": "Imports" }, { "package": "scran", "role": "Imports" }, { "package": "sys", "role": "Imports" }, { "package": "epivizrData", "role": "Imports" }, { "package": "epivizrServer", "role": "Imports" }, { "package": "ggraph", "role": "Imports" }, { "package": "scater", "role": "Imports" }, { "package": "Seurat", "role": "Imports" }, { "package": "SingleCellExperiment", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "SC3", "role": "Suggests" }, { "package": "scRNAseq", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "msd16s", "role": "Suggests" }, { "package": "metagenomeSeq", "role": "Suggests" }, { "package": "epivizrStandalone", "role": "Suggests" }, { "package": "GenomeInfoDb", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.19.0", "bioc": "3.24" }, { "branch": "release", "version": "1.18.0", "bioc": "3.23" } ], "_topics": [ "visualization", "infrastructure", "gui", "singlecell" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 342, "source": "https://www.bioconductor.org/packages/stats/bioc/scTreeViz" }, "_searchresults": 3, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/readme.html", "extra/readme.md", "extra/scTreeViz.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "aggregateTree", "ClusterHierarchy", "createFromSCE", "createFromSeurat", "createTreeViz", "getNodes", "show", "splitAt", "startTreeviz", "TreeIndex", "TreeViz" ], "_help": [ { "page": "dot-generate_hierarchy_tree", "title": "generate hierarchy tree", "topics": [ ".generate_hierarchy_tree" ] }, { "page": "dot-generate_leaf_of_table", "title": "generate leaf of table", "topics": [ ".generate_leaf_of_table" ] }, { "page": "dot-generate_node_ids", "title": "generate node ids in the tree", "topics": [ ".generate_node_ids" ] }, { "page": "dot-generate_nodes_table", "title": "generate nodes table tree", "topics": [ ".generate_nodes_table" ] }, { "page": "dot-replaceNAFeatures", "title": "replace if there are NA's in the hierarchy", "topics": [ ".replaceNAFeatures" ] }, { "page": "TreeIndex-methods", "title": "Subset TreeIndex", "topics": [ "getNodes", "getNodes,TreeIndex-method", "getNodeStates", "getNodeStates,TreeIndex-method", "show,TreeIndex-method", "splitAt", "splitAt,TreeIndex-method", "[,TreeIndex,ANY,ANY,ANY-method" ] }, { "page": "ClusterHierarchy", "title": "Creates a new ClusterHierarchy object.", "topics": [ "ClusterHierarchy" ] }, { "page": "ClusterHierarchy-class", "title": "ClusterHierarchy class to manage treeviz cluster data", "topics": [ "ClusterHierarchy-class" ] }, { "page": "createFromSCE", "title": "Creates a `TreeViz`` object from `SingleCellExperiment`. Generates clusters based on Walktrap algorithm if no default is provided", "topics": [ "createFromSCE" ] }, { "page": "createFromSeurat", "title": "Creates a `TreeViz` object from `Seurat`", "topics": [ "createFromSeurat" ] }, { "page": "createTreeViz", "title": "Creates `TreeViz` object from hierarchy and count matrix", "topics": [ "createTreeViz" ] }, { "page": "EpivizTreeData-class", "title": "Data container for MRexperiment objects", "topics": [ "EpivizTreeData", "EpivizTreeData-class" ] }, { "page": "set_gene_list", "title": "Sets gene list for visualization", "topics": [ "set_gene_list" ] }, { "page": "TreeViz-methods", "title": "show object", "topics": [ "aggregateTree", "aggregateTree,TreeViz-method", "plot,TreeViz,ANY-method", "register,TreeViz-method", "show,TreeViz-method" ] }, { "page": "startTreeviz", "title": "Start treeviz app and create 'TreeVizApp' object to manage connection.", "topics": [ "startTreeviz" ] }, { "page": "TreeIndex", "title": "create a new TreeIndex object", "topics": [ "TreeIndex" ] }, { "page": "TreeIndex-class", "title": "TreeIndex class to manage and query hierarchical data", "topics": [ "TreeIndex-class" ] }, { "page": "TreeViz", "title": "The TreeViz class.", "topics": [ "TreeViz" ] }, { "page": "TreeViz-class", "title": "TreeViz class wrapper for SummarizedExperiment objects", "topics": [ "TreeViz-class" ] }, { "page": "TreeVizApp-class", "title": "Class managing connection to metaviz application.", "topics": [ "TreeVizApp", "TreeVizApp-class" ] } ], "_readme": "https://github.com/bioc/scTreeViz/raw/HEAD/README.md", "_rundeps": [ "abind", "AnnotationDbi", "AnnotationFilter", "askpass", "assorthead", "backports", "base64enc", "beachmat", "beeswarm", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocManager", "BiocNeighbors", "BiocParallel", "BiocSingular", "Biostrings", "bit", "bit64", "bitops", "blob", "bluster", "bslib", "bumphunter", "cachem", "Cairo", "caTools", "checkmate", "cigarillo", "cli", "cluster", "clustree", "codetools", "commonmark", "cowplot", "cpp11", "crayon", "crosstalk", "curl", "data.table", "DBI", "DelayedArray", "deldir", "digest", "doRNG", "dotCall64", "dplyr", "dqrng", "edgeR", "ensembldb", "epivizr", "epivizrData", "epivizrServer", "evaluate", "farver", "fastDummies", "fastmap", "fitdistrplus", "FNN", "fontawesome", "foreach", "formatR", "fs", "futile.logger", "futile.options", "future", "future.apply", "generics", "GenomeInfoDb", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "ggbeeswarm", "ggforce", "ggplot2", "ggraph", "ggrastr", "ggrepel", "ggridges", "globals", "glue", "goftest", "gplots", "graph", "graphlayouts", "gridExtra", "gtable", "gtools", "here", "highr", "htmltools", "htmlwidgets", "httpuv", "httr", "ica", "igraph", "IRanges", "irlba", "isoband", "iterators", "jquerylib", "jsonlite", "KEGGREST", "KernSmooth", "knitr", "labeling", "lambda.r", "later", "lattice", "lazyeval", "lifecycle", "limma", "listenv", "lmtest", "locfit", "magrittr", "MASS", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "metapod", "mime", "miniUI", "nlme", "openssl", "OrganismDbi", "otel", "parallelly", "patchwork", "pbapply", "pheatmap", "pillar", "pkgconfig", "plotly", "plyr", "png", "polyclip", "progressr", "promises", "ProtGenerics", "purrr", "R6", "ragg", "RANN", "rappdirs", "RBGL", "RColorBrewer", "Rcpp", "RcppAnnoy", "RcppArmadillo", "RcppEigen", "RcppHNSW", "RcppML", "RcppProgress", "RcppTOML", "RCurl", "reshape2", "restfulr", "reticulate", "Rhtslib", "rjson", "rlang", "rmarkdown", "rngtools", "ROCR", "rprojroot", "Rsamtools", "RSpectra", "RSQLite", "rsvd", "rtracklayer", "Rtsne", "S4Arrays", "S4Vectors", "S7", "sass", "ScaledMatrix", "scales", "scater", "scattermore", "scran", "sctransform", "scuttle", "Seqinfo", "Seurat", "SeuratObject", "shiny", "SingleCellExperiment", "sitmo", "snow", "sourcetools", "sp", "spam", "SparseArray", "spatstat.data", "spatstat.explore", "spatstat.geom", "spatstat.random", "spatstat.sparse", "spatstat.univar", "spatstat.utils", "statmod", "stringi", "stringr", "SummarizedExperiment", "survival", "sys", "systemfonts", "tensor", "textshaping", "tibble", "tidygraph", "tidyr", "tidyselect", "tinytex", "tweenr", "UCSC.utils", "utf8", "uwot", "vctrs", "vipor", "viridis", "viridisLite", "withr", "xfun", "XML", "xtable", "XVector", "yaml", "zoo" ], "_vignettes": [ { "source": "ExploreTreeViz.Rmd", "filename": "ExploreTreeViz.html", "title": "Interactively explore and visualize Single Cell RNA seq data", "author": "Jayaram Kancherla, Kazi Tasnim Zinat, Héctor Corrada Bravo", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Loading required packages", "Preparing Datasets", "From SingleCellExperiment", "From Seurat", "Create TreeViz from count matrix and Cluster hierarchy", "Start the TreeViz App (using hosted app)", "Visualize gene expression across clusters", "Adding Gene Box Plots via UI", "Adding Gene Box Plots via R Session", "Stop App", "Session" ], "created": "2020-07-08 17:23:28", "modified": "2021-08-21 15:27:40", "commits": 25 } ], "_score": 4, "_indexed": true, "_nocasepkg": "sctreeviz", "_universes": [ "bioc", "jkanche" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-05-30T10:44:53.000Z", "distro": "noble", "commit": "dd15f611114a451159c57445cab5d61496dbf137", "fileid": "ba674a0479f9e437d959a0a99e5110eb6aad9a6d111ed278abfefa9293be82e1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676994996" }, { "r": "4.6.0", "os": "linux", "version": "1.19.0", "date": "2026-05-30T10:44:52.000Z", "distro": "noble", "commit": "dd15f611114a451159c57445cab5d61496dbf137", "fileid": "0f207e123fd5de3049b8c93c9b3a1c54da0221efd4dc1d12628e9c92fb896dd7", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676994996" }, { "r": "4.5.3", "os": "mac", "version": "1.19.0", "date": "2026-05-30T15:23:00.000Z", "commit": "dd15f611114a451159c57445cab5d61496dbf137", "fileid": "642e6026c9786f728849443578313efcff8434009bd55039fe91aa638c14e3b4", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676994996" }, { "r": "4.6.0", "os": "mac", "version": "1.19.0", "date": "2026-05-30T15:23:10.000Z", "commit": "dd15f611114a451159c57445cab5d61496dbf137", "fileid": "f6fa8110d552fe7b053b36a4911c42b7717ddb444fcb8ac215a659679a7ce04c", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676994996" }, { "r": "4.6.0", "os": "wasm", "version": "1.19.0", "date": "2026-05-30T10:44:22.000Z", "commit": "dd15f611114a451159c57445cab5d61496dbf137", "fileid": "d16c328783dcd5cf40d895674153bb0acb9361ca96cf49457ae237002c82e9b5", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676994996" }, { "r": "4.7.0", "os": "win", "version": "1.19.0", "date": "2026-05-30T11:04:11.000Z", "commit": "dd15f611114a451159c57445cab5d61496dbf137", "fileid": "4c46b8146ef1207b2586f6a903d4be341f043f354c1c9fc447ed6cdf88d65701", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676994996" }, { "r": "4.5.3", "os": "win", "version": "1.19.0", "date": "2026-05-30T11:02:10.000Z", "commit": "dd15f611114a451159c57445cab5d61496dbf137", "fileid": "78f1de9eb638df167289f3fe0b76ec390a2ccdb432afdf3ab43c0d0a65014d19", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676994996" }, { "r": "4.6.0", "os": "win", "version": "1.19.0", "date": "2026-05-30T10:57:15.000Z", "commit": "dd15f611114a451159c57445cab5d61496dbf137", "fileid": "c6365731053cf4b9eff8a3715f55fa5a390ea2c6b1a6c053a3373229c3c12656", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26676994996" } ] }