tomoseqr

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15

R Package for Analyzing Tomo-seq Data

Bioconductor version: Development (3.24)

`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: 0000-0003-2999-4734

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

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

Ryosuke Matsuzawa. tomoseqr: R Package for Analyzing Tomo-seq Data. doi:10.18129/B9.bioc.tomoseqr, R package version 1.17.0, https://bioconductor.org/packages/tomoseqr.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

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

## The following initializes the development version of Bioconductor
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	1.17.0
In Bioconductor since	BioC 3.15 (R-4.2) (4.5 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, r-universe

Package Archives

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

Source Package	tomoseqr_1.17.0.tar.gz
Windows Binary (x86_64)	tomoseqr_1.17.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	tomoseqr_1.17.0.tgz
macOS Binary (sonoma-arm64)	tomoseqr_1.17.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tomoseqr
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tomoseqr
Package Short Url	https://bioconductor.org/packages/tomoseqr/
Package Downloads Report	Download Stats