tomoseqr
This is the development version of tomoseqr; for the stable release version, see tomoseqr.
R Package for Analyzing Tomo-seq Data
Bioconductor version: Development (3.21)
`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:
Maintainer: Ryosuke Matsuzawa <kinakomochi.work at gmail.com>
citation("tomoseqr")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GeneExpression, RNASeq, Sequencing, Software, Spatial, Transcriptomics, Visualization |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 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 |
See More
| 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_1.11.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |