BatchSVG
This is thereleased version of BatchSVG; for the devel version, seeBatchSVG.
Identify Batch-Biased Features in Spatially Variable Genes
Bioconductor version: Release (3.22)
`BatchSVG` is a feature-based Quality Control (QC) to identify SVGs on spatial transcriptomics data with specific types of batch effect. Regarding to the spatial transcriptomics data experiments, the batch can be defined as "sample", "sex", and etc.The `BatchSVG` method is based on binomial deviance model (Townes et al, 2019) and applies cutoffs based on the number of standard deviation (nSD) of relative change in deviance and rank difference as the data-driven thresholding approach to detect the batch-biased outliers.
Author: Christine Hou [aut]
ORCID: 0009-0001-5350-0629, Kinnary Shah [aut, cre], Jacqui Thompson [aut], Stephanie C. Hicks [aut, fnd] ORCID: 0000-0002-7858-0231
Maintainer: Kinnary Shah <kinnaryshahh at gmail.com>
citation("BatchSVG")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("BatchSVG")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BatchSVG")| 01 Tutorial for spe data object | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect,QualityControl,Software,Spatial,Transcriptomics |
| Version | 1.2.0 |
| 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/BatchSVGhttps://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
FollowInstallation instructions to use this package in your R session.
| Source Package | BatchSVG_1.2.0.tar.gz |
| Windows Binary (x86_64) | BatchSVG_1.2.0.zip |
| macOS Binary (x86_64) | BatchSVG_1.2.0.tgz |
| macOS Binary (arm64) | BatchSVG_1.2.0.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 |