Introduction | Installation | Biased Feature Identification | Perform Feature Selection using featureSelect() | Visualize SVG Selection Using svg_nSD() | Identify Biased Genes Using biasDetect() | Refine SVGs by Removing Batch-Affected Outliers | R session information
Package: BatchSVG 1.5.3
Kinnary Shah
BatchSVG: Identify Batch-Biased Spatially Variable Genes
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).
Authors:
BatchSVG_1.5.3.tar.gz
BatchSVG_1.5.3.zip(r-4.7)BatchSVG_1.5.3.zip(r-4.6)BatchSVG_1.5.3.zip(r-4.5)
BatchSVG_1.5.3.tgz(r-4.6-any)BatchSVG_1.5.3.tgz(r-4.5-any)
BatchSVG_1.5.3.tar.gz(r-4.7-any)BatchSVG_1.5.3.tar.gz(r-4.6-any)
BatchSVG_1.5.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BatchSVG/json (API)
| # Install 'BatchSVG' in R: |
| install.packages('BatchSVG', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/christinehou11/batchsvg/issues
Pkgdown/docs site:https://christinehou11.github.io
Datasets:
- list_batch_df - List of data frames of nSD(s) on the batch of subject
On BioConductor:BatchSVG-1.5.3(bioc 3.24)BatchSVG-1.4.0(bioc 3.23)
spatialtranscriptomicsbatcheffectqualitycontrolbatch-effectbioconductor-packagespatial-transcriptomics
Last updated from:e95b4dd91a. Checks:1 WARNING, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 301 | ||
| linux-devel-x86_64 | OK | 605 | ||
| source / vignettes | OK | 439 | ||
| linux-release-x86_64 | OK | 562 | ||
| macos-release-arm64 | OK | 528 | ||
| macos-oldrel-arm64 | OK | 420 | ||
| windows-devel | OK | 1926 | ||
| windows-release | OK | 1546 | ||
| windows-oldrel | OK | 1831 | ||
| wasm-release | OK | 224 |
Exports:biasDetectfeatureSelectsvg_nSD
Dependencies:abindassortheadbeachmatBHBiobaseBiocGenericsBiocParallelBiocSingularclicodetoolscowplotcpp11DelayedArraydplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggrepelglmpcagluegtableIRangesirlbaisobandlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatspillarpkgconfigR6RColorBrewerRcpprlangrsvdS4ArraysS4VectorsS7ScaledMatrixscalesscrySeqinfoSingleCellExperimentsnowSparseArraySummarizedExperimenttibbletidyselectutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Biased Genes Identification | biasDetect |
| Feature selection | featureSelect |
| List of data frames of nSD(s) on the batch of subject | list_batch_df |
| SVGs Plots | svg_nSD |
