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This is the development version of tomoda; for the stable release version, see tomoda.

Tomo-seq data analysis

Bioconductor version: Development (3.19)

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.

Author: Wendao Liu [aut, cre]

Maintainer: Wendao Liu <liuwd15 at tsinghua.org.cn>

Citation (from within R, enter citation("tomoda")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

tomoda HTML R Script
Reference Manual PDF


biocViews Clustering, GeneExpression, RNASeq, Sequencing, Software, Spatial, Transcriptomics, Visualization
Version 1.13.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License MIT + file LICENSE
Depends R (>= 4.0.0)
Imports methods, stats, grDevices, reshape2, Rtsne, umap, RColorBrewer, ggplot2, ggrepel, SummarizedExperiment
System Requirements
URL https://github.com/liuwd15/tomoda
Bug Reports https://github.com/liuwd15/tomoda/issues
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Suggests knitr, rmarkdown, BiocStyle, testthat
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Follow Installation instructions to use this package in your R session.

Source Package tomoda_1.13.0.tar.gz
Windows Binary tomoda_1.13.0.zip
macOS Binary (x86_64) tomoda_1.13.0.tgz
macOS Binary (arm64) tomoda_1.13.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/tomoda
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tomoda
Bioc Package Browser https://code.bioconductor.org/browse/tomoda/
Package Short Url https://bioconductor.org/packages/tomoda/
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