tomoda

DOI: 10.18129/B9.bioc.tomoda  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see tomoda.

Tomo-seq data analysis

Bioconductor version: 3.16

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>

Installation

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

 

HTML	R Script	tomoda
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Clustering, GeneExpression, RNASeq, Sequencing, Software, Spatial, Transcriptomics, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.12 (R-4.0) (2.5 years)
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	tomoda_1.8.0.tar.gz
Windows Binary	tomoda_1.8.0.zip
macOS Binary (x86_64)	tomoda_1.8.0.tgz
macOS Binary (arm64)	tomoda_1.8.0.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