BatchSVG
This is the released version of BatchSVG; for the devel version, see BatchSVG.
Identify Batch-Biased Spatially Variable Genes
Bioconductor version: Release (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).
Author: Christine Hou [aut]
, Kinnary Shah [aut, cre], Jacqueline R. Thompson [aut], Stephanie C. Hicks [aut, fnd]
Maintainer: Kinnary Shah <kinnaryshahh at gmail.com>
citation("BatchSVG")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 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_1.4.0.tar.gz |
| Windows Binary (x86_64) | BatchSVG_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | BatchSVG_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | BatchSVG_1.4.0.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 |