tomoda

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

Tomo-seq data analysis

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DOI: 10.18129/B9.bioc.tomoda

Bioconductor version: Development (3.23)

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.201601006) 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] ORCID iD ORCID: 0000-0002-5124-9338

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

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

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("tomoda")

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