tomoda
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see tomoda.
Tomo-seq data analysis
Bioconductor version: 3.17
This package provides many easy-to-use methods to analyze and visualize tomo-seq data. The tomo-seq technique is based on cryosectioning of tissue and performing RNA-seq on consecutive sections. (Reference: Kruse F, Junker JP, van Oudenaarden A, Bakkers J. Tomo-seq: A method to obtain genome-wide expression data with spatial resolution. Methods Cell Biol. 2016;135:299-307. doi:10.1016/bs.mcb.2016.01.006) The main purpose of the package is to find zones with similar transcriptional profiles and spatially expressed genes in a tomo-seq sample. Several visulization functions are available to create easy-to-modify plots.
Author: Wendao Liu [aut, cre] 
Maintainer: Wendao Liu <liuwd15 at tsinghua.org.cn>
citation("tomoda")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("tomoda")
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("tomoda")| tomoda | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Clustering, GeneExpression, RNASeq, Sequencing, Software, Spatial, Transcriptomics, Visualization |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.0.0) |
| Imports | methods, stats, grDevices, reshape2, Rtsne, umap, RColorBrewer, ggplot2, ggrepel, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/liuwd15/tomoda |
| Bug Reports | https://github.com/liuwd15/tomoda/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle, testthat |
| 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 | tomoda_1.10.0.tar.gz |
| Windows Binary | tomoda_1.10.0.zip |
| macOS Binary (x86_64) | tomoda_1.10.0.tgz |
| macOS Binary (arm64) | tomoda_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tomoda |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tomoda |
| Bioc Package Browser | https://code.bioconductor.org/browse/tomoda/ |
| Package Short Url | https://bioconductor.org/packages/tomoda/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |