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tomoseqr

R Package for Analyzing Tomo-seq Data


Bioconductor version: Release (3.18)

`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>

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

Installation

To install this package, start R (version "4.3") 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")
tomoseqr HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GeneExpression, RNASeq, Sequencing, Software, Spatial, Transcriptomics, Visualization
Version 1.6.0
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License MIT + file LICENSE
Depends R (>= 4.2)
Imports grDevices, graphics, animation, tibble, dplyr, stringr, purrr, methods, shiny, BiocFileCache, readr, tools, plotly, ggplot2
System Requirements
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Suggests rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0)
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Package Archives

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

Source Package tomoseqr_1.6.0.tar.gz
Windows Binary tomoseqr_1.6.0.zip
macOS Binary (x86_64) tomoseqr_1.6.0.tgz
macOS Binary (arm64) tomoseqr_1.6.0.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