tomoda

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 (3.15)

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 <liuwd15 at tsinghua.org.cn>

Maintainer: <>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews Clustering, GeneExpression, RNASeq, Sequencing, Software, Transcriptomics, Visualization
Version 1.5.0
In Bioconductor since BioC 3.12 (R-4.0) (1 year)
License MIT + file LICENSE
Depends R (>= 4.0.0)
Imports methods, stats, grDevices, reshape2, Rtsne, umap, RColorBrewer, ggplot2, ggrepel, SummarizedExperiment
LinkingTo
Suggests knitr, rmarkdown, BiocStyle, testthat
SystemRequirements
Enhances
URL https://github.com/liuwd15/tomoda
BugReports https://github.com/liuwd15/tomoda/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS 10.13 (High Sierra)
Source Repository git clone https://git.bioconductor.org/packages/tomoda
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/tomoda
Package Short Url https://bioconductor.org/packages/tomoda/
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