{ "_id": "6a1bdfaa1d7bb097a0a17ddd", "Package": "tomoda", "Title": "Tomo-seq data analysis", "Version": "1.22.0", "Authors@R": "person(given = \"Wendao\",\nfamily = \"Liu\",\nrole = c(\"aut\", \"cre\"),\nemail = \"liuwd15@tsinghua.org.cn\",\ncomment = c(ORCID = \"0000-0002-5124-9338\"))", "Description": "This package provides many easy-to-use methods to analyze\nand visualize tomo-seq data. The tomo-seq technique is based on\ncryosectioning of tissue and performing RNA-seq on consecutive\nsections. (Reference: Kruse F, Junker JP, van Oudenaarden A,\nBakkers J. Tomo-seq: A method to obtain genome-wide expression\ndata with spatial resolution. Methods Cell Biol.\n2016;135:299-307. doi:10.1016/bs.mcb.2016.01.006) The main\npurpose of the package is to find zones with similar\ntranscriptional profiles and spatially expressed genes in a\ntomo-seq sample. Several visulization functions are available\nto create easy-to-modify plots.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.1.2", "URL": "https://github.com/liuwd15/tomoda", "BugReports": "https://github.com/liuwd15/tomoda/issues", "biocViews": "GeneExpression, Sequencing, RNASeq, Transcriptomics,\nSpatial, Clustering, Visualization", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libicu-dev libpng-dev libssl-dev python3 zlib1g-dev", "Repository": "https://bioc-release.r-universe.dev", "Date/Publication": "2026-04-28 12:53:56 UTC", "RemoteUrl": "https://github.com/bioc/tomoda", "RemoteRef": "RELEASE_3_23", "RemoteSha": "954c16794c826904c582633c3678fb800740329d", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-31 06:35:31 UTC", "User": "root" }, "Author": "Wendao Liu [aut, cre] (ORCID: )", "Maintainer": "Wendao Liu ", "MD5sum": "043c56af359c3c84a9812378d657833a", "_user": "bioc-release", "_type": "src", "_file": "tomoda_1.22.0.tar.gz", "_fileid": "f4a3dadcc8f5baf9567b8f5e67722f452e43b6868192b137d8e224f15745e287", "_filesize": 2859995, "_sha256": "f4a3dadcc8f5baf9567b8f5e67722f452e43b6868192b137d8e224f15745e287", "_created": "2026-05-31T06:35:31.000Z", "_published": "2026-05-31T07:13:46.284Z", "_jobs": [ { "job": 78705985663, "time": 179, "config": "bioc-checks", "r": "4.6.0", "check": "NOTE", "artifact": "7314494169" }, { "job": 78705985673, "time": 431, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7314520618" }, { "job": 78705985670, "time": 384, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7314516107" }, { "job": 78705985655, "time": 259, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7314704612" }, { "job": 78705985667, "time": 239, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7314695889" }, { "job": 78705706668, "time": 281, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7314473259" }, { "job": 78705985656, "time": 123, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7314487908" }, { "job": 78705985686, "time": 327, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7314510509" }, { "job": 78705985684, "time": 296, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7314507294" }, { "job": 78705985685, "time": 323, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7314510227" } ], "_bioccheck": { "error": 0, "warning": 0, "note": 7 }, "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705429003", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/tomoda", "_commit": { "id": "954c16794c826904c582633c3678fb800740329d", "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": 1777380836 }, "_maintainer": { "name": "Wendao Liu", "email": "liuwd15@tsinghua.org.cn", "orcid": "0000-0002-5124-9338" }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0.0", "role": "Depends" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "reshape2", "role": "Imports" }, { "package": "Rtsne", "role": "Imports" }, { "package": "umap", "role": "Imports" }, { "package": "RColorBrewer", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "ggrepel", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "BiocStyle", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 1 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.23.0", "bioc": "3.24" }, { "branch": "release", "version": "1.22.0", "bioc": "3.23" } ], "_topics": [ "geneexpression", "sequencing", "rnaseq", "transcriptomics", "spatial", "clustering", "visualization" ], "_stars": 0, "_contributors": [ { "user": "liuwd15", "count": 21, "uuid": 28178504 }, { "user": "nturaga", "count": 6, "uuid": 2746443 } ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 326, "source": "https://www.bioconductor.org/packages/stats/bioc/tomoda" }, "_devurl": "https://github.com/liuwd15/tomoda", "_searchresults": 3, "_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/tomoda.html", "manual.pdf" ], "_homeurl": "https://github.com/liuwd15/tomoda", "_realowner": "bioc", "_cranurl": false, "_exports": [ "corHeatmap", "createTomo", "embedPlot", "expHeatmap", "findPeak", "findPeakGene", "geneCorHeatmap", "geneEmbedPlot", "hierarchClust", "kmeansClust", "linePlot", "normalizeTomo", "runPCA", "runTSNE", "runUMAP", "scaleTomo", "tomoMatrix", "tomoSummarizedExperiment" ], "_datasets": [ { "name": "zh.data", "title": "A raw read count matrix of zebrafish injured heart.", "object": "zh.data", "file": "zh.data.RData", "class": [ "matrix", "array" ], "fields": [ "X1", "X2", "X3", "X4", "X5", "X6", "X7", "X8", "X9", "X10", "X11", "X12", "X13", "X14", "X15", "X16", "X17", "X18", "X19", "X20", "X21", "X22", "X23", "X24", "X25", "X26", "X27", "X28", "X29", "X30", "X31", "X32", "X33", "X34", "X35", "X36", "X37", "X38", "X39", "X40" ], "rows": 16495, "table": true, "tojson": true } ], "_help": [ { "page": "corHeatmap", "title": "Correlation heatmap of sections", "topics": [ "corHeatmap" ] }, { "page": "createTomo", "title": "Create an object representing tomo-seq data", "topics": [ "createTomo", "createTomo,matrix-method", "createTomo,missing-method", "createTomo,SummarizedExperiment-method" ] }, { "page": "embedPlot", "title": "Embedding plot for sections", "topics": [ "embedPlot" ] }, { "page": "expHeatmap", "title": "Expression heatmap", "topics": [ "expHeatmap" ] }, { "page": "findPeak", "title": "Find peak in a vector", "topics": [ "findPeak" ] }, { "page": "findPeakGene", "title": "Find peak genes", "topics": [ "findPeakGene" ] }, { "page": "geneCorHeatmap", "title": "Correlation heatmap of genes", "topics": [ "geneCorHeatmap" ] }, { "page": "geneEmbedPlot", "title": "Embedding plot for genes", "topics": [ "geneEmbedPlot" ] }, { "page": "hierarchClust", "title": "Hierarchical clustering across sections", "topics": [ "hierarchClust" ] }, { "page": "kmeansClust", "title": "K-Means clustering across sections", "topics": [ "kmeansClust" ] }, { "page": "linePlot", "title": "Line plot for expression traces", "topics": [ "linePlot" ] }, { "page": "normalizeTomo", "title": "Normalize data", "topics": [ "normalizeTomo" ] }, { "page": "runPCA", "title": "Perform PCA", "topics": [ "runPCA" ] }, { "page": "runTSNE", "title": "Perform TSNE", "topics": [ "runTSNE" ] }, { "page": "runUMAP", "title": "Perform UMAP", "topics": [ "runUMAP" ] }, { "page": "scaleTomo", "title": "Scale data", "topics": [ "scaleTomo" ] }, { "page": "tomoMatrix", "title": "Create an object from matrix", "topics": [ "tomoMatrix" ] }, { "page": "tomoSummarizedExperiment", "title": "Create an object from SummarizedExperiment", "topics": [ "tomoSummarizedExperiment" ] }, { "page": "zh.data", "title": "A raw read count matrix of zebrafish injured heart.", "topics": [ "zh.data" ] } ], "_readme": "https://github.com/bioc/tomoda/raw/RELEASE_3_23/README.md", "_rundeps": [ "abind", "askpass", "Biobase", "BiocGenerics", "cli", "cpp11", "DelayedArray", "farver", "generics", "GenomicRanges", "ggplot2", "ggrepel", "glue", "gtable", "here", "IRanges", "isoband", "jsonlite", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "openssl", "plyr", "png", "R6", "rappdirs", "RColorBrewer", "Rcpp", "RcppEigen", "RcppTOML", "reshape2", "reticulate", "rlang", "rprojroot", "RSpectra", "Rtsne", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SparseArray", "stringi", "stringr", "SummarizedExperiment", "sys", "umap", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "tomoda.Rmd", "filename": "tomoda.html", "title": "tomoda for tomo-seq data analysis", "author": "Wendao Liu", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Background", "Dataset", "Preprocessing", "Create an object", "Normalize and scale data", "Find zones with different transcriptional profiles", "Correlation analysis", "Dimensionality reduction analysis", "Clustering analysis", "Analyze peak genes", "Find peak genes", "Find co-regulated genes", "Plot expression traces of genes", "Modify plots", "Session Information" ], "created": "2020-09-14 10:09:23", "modified": "2020-10-13 06:06:37", "commits": 5 } ], "_score": 4, "_indexed": false, "_nocasepkg": "tomoda", "_universes": [ "bioc-release" ], "_indexurl": "https://bioc.r-universe.dev/tomoda", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.22.0", "date": "2026-05-31T06:39:11.000Z", "distro": "noble", "commit": "954c16794c826904c582633c3678fb800740329d", "fileid": "c657bf1d5543e9eb014dbefe84258fec119f53bf5f17939fee159f6f7f221323", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705429003" }, { "r": "4.6.0", "os": "linux", "version": "1.22.0", "date": "2026-05-31T06:38:37.000Z", "distro": "noble", "commit": "954c16794c826904c582633c3678fb800740329d", "fileid": "385250e284ef38db3e8b99c3757a1de0c0e79e6d20198d97110d6e494a060a33", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705429003" }, { "r": "4.5.3", "os": "mac", "version": "1.22.0", "date": "2026-05-31T07:10:33.000Z", "commit": "954c16794c826904c582633c3678fb800740329d", "fileid": "82b17d11fd2634bfa3dba30aa19d41b01f501c05ae5d5a2a31fc4887ae1404ff", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705429003" }, { "r": "4.6.0", "os": "mac", "version": "1.22.0", "date": "2026-05-31T07:09:26.000Z", "commit": "954c16794c826904c582633c3678fb800740329d", "fileid": "970493ad54a5532889925df557094cdb6e4c0dafaa3f266f84d41c3b031f6122", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705429003" }, { "r": "4.6.0", "os": "wasm", "version": "1.22.0", "date": "2026-05-31T06:38:09.000Z", "commit": "954c16794c826904c582633c3678fb800740329d", "fileid": "c4ae4f22e905fa1aa910737536e76edbc18a85ced8bac655db64655cc32fe885", "status": "success", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705429003" }, { "r": "4.7.0", "os": "win", "version": "1.22.0", "date": "2026-05-31T06:37:12.000Z", "commit": "954c16794c826904c582633c3678fb800740329d", "fileid": "cb06292bd2e4c622541f47fe7b73390123589c20a38d9af40328d0d85ae9e1c0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705429003" }, { "r": "4.5.3", "os": "win", "version": "1.22.0", "date": "2026-05-31T06:37:30.000Z", "commit": "954c16794c826904c582633c3678fb800740329d", "fileid": "7a7467369a0edca882c3911feed9f14c9f8b4b29dd25e347c2963eee4ce87a24", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705429003" }, { "r": "4.6.0", "os": "win", "version": "1.22.0", "date": "2026-05-31T06:37:06.000Z", "commit": "954c16794c826904c582633c3678fb800740329d", "fileid": "61adafd5c02e6cfab43758ecd0b92c09267d5c5ea3b11d83abd41cd74f6dae24", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26705429003" } ] }