BatchSVG
This is the development version of BatchSVG; for the stable release version, see BatchSVG.
Identify Batch-Biased Spatially Variable Genes
Bioconductor version: Development (3.23)
`BatchSVG` is a method to identify batch-biased spatially variable genes (SVGs) in spatial transcriptomics data. The batch variable can be defined as "sample", "donor sex", or other batch effects of interest. The `BatchSVG` method is based on the binomial deviance model ([Townes et al, 2019](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1861-6))).
Author: Christine Hou [aut]
, Kinnary Shah [aut, cre], Jacqui Thompson [aut], Stephanie C. Hicks [aut, fnd]
Maintainer: Kinnary Shah <kinnaryshahh at gmail.com>
citation("BatchSVG")):
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("BatchSVG")
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("BatchSVG")| Tutorial for spe object | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, QualityControl, Software, Spatial, Transcriptomics |
| Version | 1.3.2 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0) |
| Imports | scry, dplyr, stats, rlang, cowplot, ggrepel, ggplot2, RColorBrewer, scales, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/christinehou11/BatchSVG https://christinehou11.github.io/BatchSVG |
| Bug Reports | https://github.com/christinehou11/BatchSVG/issues |
See More
| Suggests | testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, spatialLIBD |
| 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 | BatchSVG_1.3.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | BatchSVG_1.3.0.tgz |
| macOS Binary (arm64) | BatchSVG_1.3.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BatchSVG |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BatchSVG |
| Bioc Package Browser | https://code.bioconductor.org/browse/BatchSVG/ |
| Package Short Url | https://bioconductor.org/packages/BatchSVG/ |
| Package Downloads Report | Download Stats |