tomoseqr

This is the development version of tomoseqr; for the stable release version, see tomoseqr.

R Package for Analyzing Tomo-seq Data

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.tomoseqr

Bioconductor version: Development (3.23)

`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] ORCID iD ORCID: 0000-0003-2999-4734

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

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

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, RNASeq, Sequencing, Software, Spatial, Transcriptomics, Visualization

Version 1.15.0

In Bioconductor since BioC 3.15 (R-4.2) (3.5 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

URL

Suggests rmarkdown, knitr, BiocStyle, testthat (>= 3.0.0)

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 tomoseqr_1.15.0.tar.gz

Windows Binary (x86_64) tomoseqr_1.15.0.zip

macOS Binary (x86_64) tomoseqr_1.15.0.tgz

macOS Binary (arm64) tomoseqr_1.15.0.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