tomoseqr

DOI: 10.18129/B9.bioc.tomoseqr  

R Package for Analyzing Tomo-seq Data

Bioconductor version: Release (3.16)

`tomoseqr` is an R package for analyzing Tomo-seq data. Tomo-seq is a genome-wide RNA tomography method that combines combining high-throughput RNA sequencing with cryosectioning for spatially resolved transcriptomics. `tomoseqr` reconstructs 3D expression patterns from tomo-seq data and visualizes the reconstructed 3D expression patterns.

Author: Ryosuke Matsuzawa [aut, cre]

Maintainer: Ryosuke Matsuzawa <kinakomochi.work at gmail.com>

Installation

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

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

BiocManager::install("tomoseqr")

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("tomoseqr")

 

HTML	R Script	tomoseqr
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpression, RNASeq, Sequencing, Software, Spatial, Transcriptomics, Visualization
Version	1.2.0
In Bioconductor since	BioC 3.15 (R-4.2) (1 year)
License	MIT + file LICENSE
Depends	R (>= 4.2)
Imports	grDevices, graphics, animation, tibble, dplyr, stringr, purrr, methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2
LinkingTo
Suggests	rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL
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	tomoseqr_1.2.0.tar.gz
Windows Binary	tomoseqr_1.2.0.zip
macOS Binary (x86_64)	tomoseqr_1.2.0.tgz
macOS Binary (arm64)	tomoseqr_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tomoseqr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tomoseqr
Bioc Package Browser	https://code.bioconductor.org/browse/tomoseqr/
Package Short Url	https://bioconductor.org/packages/tomoseqr/
Package Downloads Report	Download Stats