DOI: 10.18129/B9.bioc.tomoda    

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

Tomo-seq data analysis

Bioconductor version: Development (3.17)

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>

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


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biocViews Clustering, GeneExpression, RNASeq, Sequencing, Software, Spatial, Transcriptomics, Visualization
Version 1.9.0
In Bioconductor since BioC 3.12 (R-4.0) (2 years)
License MIT + file LICENSE
Depends R (>= 4.0.0)
Imports methods, stats, grDevices, reshape2, Rtsne, umap, RColorBrewer, ggplot2, ggrepel, SummarizedExperiment
Suggests knitr, rmarkdown, BiocStyle, testthat
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