Package: tomoda
Title: Tomo-seq data analysis
Version: 1.21.0
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
git_url: https://git.bioconductor.org/packages/tomoda
git_branch: devel
git_last_commit: 2682c14
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
