tomoda

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see tomoda.

Tomo-seq data analysis


Bioconductor version: 3.18

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 "4.3") 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")
tomoda HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Clustering, GeneExpression, RNASeq, Sequencing, Software, Spatial, Transcriptomics, Visualization
Version 1.12.0
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
See More
Suggests knitr, rmarkdown, BiocStyle, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package tomoda_1.12.0.tar.gz
Windows Binary tomoda_1.12.0.zip
macOS Binary (x86_64) tomoda_1.12.0.tgz
macOS Binary (arm64) tomoda_1.12.0.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