Package: tomoda
Title: Tomo-seq data analysis
Version: 1.23.0
Authors@R: 
    person(given = "Wendao",
           family = "Liu",
           role = c("aut", "cre"),
           email = "liuwd15@tsinghua.org.cn",
		   comment = c(ORCID = "0000-0002-5124-9338"))
Description: This package provides many easy-to-use methods to analyze
        and visualize tomo-seq data. The tomo-seq technique is based on
        cryosectioning of tissue and performing RNA-seq on consecutive
        sections. (Reference: Kruse F, Junker JP, van Oudenaarden A,
        Bakkers J. Tomo-seq: A method to obtain genome-wide expression
        data with spatial resolution. Methods Cell Biol.
        2016;135:299-307. doi:10.1016/bs.mcb.2016.01.006) The main
        purpose of the package is to find zones with similar
        transcriptional profiles and spatially expressed genes in a
        tomo-seq sample. Several visulization functions are available
        to create easy-to-modify plots.
Depends: R (>= 4.0.0)
Imports: methods, stats, grDevices, reshape2, Rtsne, umap,
        RColorBrewer, ggplot2, ggrepel, SummarizedExperiment
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Suggests: knitr, rmarkdown, BiocStyle, testthat
URL: https://github.com/liuwd15/tomoda
BugReports: https://github.com/liuwd15/tomoda/issues
biocViews: GeneExpression, Sequencing, RNASeq, Transcriptomics,
        Spatial, Clustering, Visualization
VignetteBuilder: knitr
Config/pak/sysreqs: libicu-dev libpng-dev libssl-dev python3 zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:53:56 UTC
RemoteUrl: https://github.com/bioc/tomoda
RemoteRef: HEAD
RemoteSha: 96ce4ba71e98ef7c1fc2f4122030562b44c1874f
NeedsCompilation: no
Packaged: 2026-07-04 22:46:37 UTC; root
Author: Wendao Liu [aut, cre] (ORCID: <https://orcid.org/0000-0002-5124-9338>)
Maintainer: Wendao Liu <liuwd15@tsinghua.org.cn>