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tomoda

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")):

Installation

To install this package, start R (version "4.4") 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.

Documentation

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

browseVignettes("tomoda")
tomoda HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

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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Package Archives

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/
Package Downloads Report Download Stats