{ "_id": "6a3a30326265ec60d6204545", "Package": "veloviz", "Title": "VeloViz: RNA-velocity informed 2D embeddings for visualizing\ncell state trajectories", "Version": "1.19.0", "Authors@R": "c(person(given = \"Lyla\",\nfamily = \"Atta\",\nrole = c(\"aut\", \"cre\"),\nemail = \"lylaatta@jhmi.edu\",\ncomment = c(ORCID = \"0000-0002-6113-0082\")),\nperson(given = \"Jean\",\nfamily = \"Fan\",\nrole = c(\"aut\"),\nemail = \"jeanfan@jhu.edu\",\ncomment = c(ORCID = \"0000-0002-0212-5451\")),\nperson(given = \"Arpan\",\nfamily = \"Sahoo\",\nrole = c(\"aut\"),\nemail = \"asahoo1@jhu.edu\",\ncomment = c(ORCID = \"0000-0002-0325-2073\")))", "Description": "VeloViz uses each cell’s current observed and predicted\nfuture transcriptional states inferred from RNA velocity\nanalysis to build a nearest neighbor graph between cells in the\npopulation. Edges are then pruned based on a cosine correlation\nthreshold and/or a distance threshold and the resulting graph\nis visualized using a force-directed graph layout algorithm.\nVeloViz can help ensure that relationships between cell states\nare reflected in the 2D embedding, allowing for more reliable\nrepresentation of underlying cellular trajectories.", "biocViews": "Transcriptomics, Visualization, GeneExpression, Sequencing,\nRNASeq, DimensionReduction", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "false", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.1.1", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libglpk-dev libxml2-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:56:42 UTC", "RemoteUrl": "https://github.com/bioc/veloviz", "RemoteRef": "HEAD", "RemoteSha": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-23 06:51:30 UTC", "User": "root" }, "Author": "Lyla Atta [aut, cre] (ORCID: ),\nJean Fan [aut] (ORCID: ),\nArpan Sahoo [aut] (ORCID: )", "Maintainer": "Lyla Atta ", "MD5sum": "4f83f33a62ee501c221a07ecd0abe7b4", "_user": "bioc", "_type": "src", "_file": "veloviz_1.19.0.tar.gz", "_fileid": "71dda9a923679b5af11f65af180f55ae0262e0d71808c6221f76efd42479055e", "_filesize": 3648995, "_sha256": "71dda9a923679b5af11f65af180f55ae0262e0d71808c6221f76efd42479055e", "_created": "2026-06-23T06:51:30.000Z", "_published": "2026-06-23T07:05:22.176Z", "_jobs": [ { "job": 82894215788, "time": 786, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7813724580" }, { "job": 82894215876, "time": 154, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "7813535603" }, { "job": 82894215833, "time": 224, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7813555946" }, { "job": 82894215865, "time": 157, "config": "linux-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7813536055" }, { "job": 82894215845, "time": 180, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7813542345" }, { "job": 82894215866, "time": 90, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7813513959" }, { "job": 82894215890, "time": 365, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "7813598390" }, { "job": 82894215877, "time": 104, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7813518121" }, { "job": 82894215864, "time": 257, "config": "macos-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7813566507" }, { "job": 82893744303, "time": 188, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7813485777" }, { "job": 82894215832, "time": 122, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7813523222" }, { "job": 82894215893, "time": 146, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7813531834" }, { "job": 82894215834, "time": 127, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7813525411" }, { "job": 82894215825, "time": 135, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7813528627" } ], "_bioccheck": { "error": 0, "warning": 1, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/28007813771", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/veloviz", "_commit": { "id": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777381002 }, "_maintainer": { "name": "Lyla Atta", "email": "lylaatta@jhmi.edu", "orcid": "0000-0002-6113-0082" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "Rcpp", "role": "Imports" }, { "package": "Matrix", "role": "Imports" }, { "package": "igraph", "role": "Imports" }, { "package": "mgcv", "role": "Imports" }, { "package": "RSpectra", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "testthat", "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": [ "transcriptomics", "visualization", "geneexpression", "sequencing", "rnaseq", "dimensionreduction", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "followers": 441, "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_searchresults": 6, "_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/veloviz.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "asNNGraph", "buildVeloviz", "graphViz", "normalizeDepth", "normalizeVariance", "plotEmbedding", "plotVeloviz", "projectedNeighbors", "reduceDimensions" ], "_datasets": [ { "name": "pancreas", "title": "Pancreas scRNA-seq data", "object": "pancreas", "file": "pancreas.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "vel", "title": "MERFISH velocity subset", "object": "vel", "file": "vel.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "asNNGraph", "title": "Function to produce idx and dist representation of a VeloViz graph", "topics": [ "asNNGraph" ] }, { "page": "buildVeloviz", "title": "Creates VeloViz graph and FDG layout from PC scores of current and projected transcriptional states.", "topics": [ "buildVeloviz" ] }, { "page": "graphViz", "title": "Visualize as velocity informed force directed graph", "topics": [ "graphViz" ] }, { "page": "normalizeDepth", "title": "Normalizes counts to CPM", "topics": [ "normalizeDepth" ] }, { "page": "normalizeVariance", "title": "Identify overdispersed genes by normalizing counts per million (CPM) gene expression variance relative to transcriptome-wide expectations (Modified from SCDE/PAGODA2 code)", "topics": [ "normalizeVariance" ] }, { "page": "pancreas", "title": "Pancreas scRNA-seq data", "topics": [ "pancreas" ] }, { "page": "plotEmbedding", "title": "Plot 2D embedding From scde/pagoda2/MUDAN", "topics": [ "plotEmbedding" ] }, { "page": "plotVeloviz", "title": "Plot function", "topics": [ "plotVeloviz" ] }, { "page": "projectedNeighbors", "title": "Computes composite distances between all cell pairs and returns k-nearest neighbors and edge weights needed to build VeloViz graph.", "topics": [ "projectedNeighbors" ] }, { "page": "reduceDimensions", "title": "Reduce dimension using Principal Components Analysis via 'svds' from 'RSpectra'", "topics": [ "reduceDimensions" ] }, { "page": "vel", "title": "MERFISH velocity subset", "topics": [ "vel" ] }, { "page": "veloviz", "title": "veloviz", "topics": [ "veloviz" ] } ], "_readme": "https://github.com/bioc/veloviz/raw/HEAD/README.md", "_rundeps": [ "cli", "cpp11", "glue", "igraph", "lattice", "lifecycle", "magrittr", "Matrix", "mgcv", "nlme", "pkgconfig", "Rcpp", "RcppEigen", "rlang", "RSpectra", "vctrs" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "vignette.Rmd", "filename": "vignette.html", "title": "VeloViz Vignette", "author": "Lyla Atta", "engine": "knitr::rmarkdown", "headings": [ "Installation", "Introduction" ], "created": "2021-05-05 17:24:37", "modified": "2021-07-14 03:34:57", "commits": 8 } ], "_score": 4, "_indexed": true, "_nocasepkg": "veloviz", "_universes": [ "bioc" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-06-23T06:53:58.000Z", "distro": "noble", "arch": "aarch64", "commit": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "fileid": "d6fa6d9993aa911c23e8ffe9844f214d6d4b64ad7fd53116390692a4e075c18d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007813771" }, { "r": "4.7.0", "os": "linux", "version": "1.19.0", "date": "2026-06-23T06:54:52.000Z", "distro": "noble", "arch": "x86_64", "commit": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "fileid": "5da91b178e0530f1a12d7e658d6019b5a776d96f7f10dbe111989e9c00c5b0fa", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007813771" }, { "r": "4.6.0", "os": "linux", "version": "1.19.0", "date": "2026-06-23T06:53:59.000Z", "distro": "noble", "arch": "aarch64", "commit": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "fileid": "98ae1e59d930fa6acf10ccda9f6d7f577c669953211f5282fd730a513a87d14d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007813771" }, { "r": "4.6.0", "os": "linux", "version": "1.19.0", "date": "2026-06-23T06:54:13.000Z", "distro": "noble", "arch": "x86_64", "commit": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "fileid": "bf3b25b57d8418db61e7d103c2107520c96cf45010a62c7e1378c98d195ff52a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007813771" }, { "r": "4.5.3", "os": "mac", "version": "1.19.0", "date": "2026-06-23T06:52:59.000Z", "arch": "aarch64", "commit": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "fileid": "7a55ef29b6ee6578646dd2511d6b8eaf9b312e789af4659d7a741fb6dd1f5743", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007813771" }, { "r": "4.5.3", "os": "mac", "version": "1.19.0", "date": "2026-06-23T06:55:46.000Z", "arch": "x86_64", "commit": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "fileid": "6b457143b6a051dca1d2ea1b20850449b7c7ca5db0db09f0b503cf9dc3aa9479", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007813771" }, { "r": "4.6.0", "os": "mac", "version": "1.19.0", "date": "2026-06-23T06:53:09.000Z", "arch": "aarch64", "commit": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "fileid": "675b954483106f5879466d9802c04e0301aeac54ae0ddc3accc3dc0e1020cf80", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007813771" }, { "r": "4.6.0", "os": "mac", "version": "1.19.0", "date": "2026-06-23T06:54:52.000Z", "arch": "x86_64", "commit": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "fileid": "93a78a42843034b6f696e71dbb7efda76da2a08c824ebe277a15df4f251f10c0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007813771" }, { "r": "4.6.0", "os": "wasm", "version": "1.19.0", "date": "2026-06-23T06:53:50.000Z", "arch": "emscripten", "commit": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "fileid": "3b634f4a9210e0c630147744c4116323ca70779affa1c62fde481d9cdde724a1", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007813771" }, { "r": "4.7.0", "os": "win", "version": "1.19.0", "date": "2026-06-23T06:53:04.000Z", "arch": "x86_64", "commit": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "fileid": "fab35ba70508252c1a2897bde5f085800c7ee8f573b5eb2da4175f2c0fff8846", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007813771" }, { "r": "4.5.3", "os": "win", "version": "1.19.0", "date": "2026-06-23T06:52:49.000Z", "arch": "x86_64", "commit": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "fileid": "0495f0fa8260b56ae714421bdc82ecddce10016c4778ee8f39437be9d588a81d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007813771" }, { "r": "4.6.0", "os": "win", "version": "1.19.0", "date": "2026-06-23T06:53:04.000Z", "arch": "x86_64", "commit": "69af4542bfe8ba0e6d554c87a2c80a0ee4aa408e", "fileid": "14c4895f27484870b6a6b09d76a801003ce9fcfe7c08f5af2a0a1df91ba0c638", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc/actions/runs/28007813771" } ] }