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Bioconductor - tomoda

tomoda

This is the released version of tomoda; for the devel version, see tomoda.

Tomo-seq data analysis

Bioconductor version: Release (3.21)

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] 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 "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")
Details biocViews Clustering, GeneExpression, RNASeq, Sequencing, Software, Spatial, Transcriptomics, Visualization Version 1.18.0 In Bioconductor since BioC 3.12 (R-4.0) (4.5 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 See More Package Archives

Follow Installation instructions to use this package in your R session.


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