anglemania
Feature Extraction for scRNA-seq Dataset Integration
Bioconductor version: 3.24 · Package version: 1.3.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
anglemania extracts genes from multi-batch scRNA-seq experiments for downstream dataset integration. It shows improvement over the conventional usage of highly-variable genes for many integration tasks. We leverage gene-gene correlations that are stable across batches to identify biologically informative genes which are less affected by batch effects. Currently, its main use is for single-cell RNA-seq dataset integration, but it can be applied for other multi-batch downstream analyses such as NMF.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("anglemania")Details
| Maintainer | Aaron Kollotzek <aaron.kollotzek@mdc-berlin.de> |
| Author | Aaron Kollotzek [aut, cre] (ORCID: <https://orcid.org/0009-0009-7142-4015>), Vedran Franke [aut] (ORCID: <https://orcid.org/0000-0003-3606-6792>), Artem Baranovskii [aut], Altuna Akalin [aut], SFB1588 [fnd] (Funded by the DFG – Deutsche Forschungsgemeinschaft) |
| License | GPL (>= 3) |
| URL | https://github.com/BIMSBbioinfo/anglemania/ |
| Bug Reports | https://github.com/BIMSBbioinfo/anglemania/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | BatchEffect, FeatureExtraction, MultipleComparison, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/anglemania/ |
Citation
From within R, enter citation("anglemania"):
Aaron Kollotzek, Vedran Franke, Artem Baranovskii, Altuna Akalin. anglemania: Feature Extraction for scRNA-seq Dataset Integration. doi:10.18129/B9.bioc.anglemania, R package version 1.3.0, https://bioconductor.org/packages/anglemania.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | anglemania_1.3.0.tar.gz |
| Windows binary (x86_64) | anglemania_1.3.0.zip |
| macOS binary (arm64) | anglemania_1.3.0.tgz |
| macOS binary (x86_64) | anglemania_1.3.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: bigparallelr, bigstatsr, checkmate, digest, dplyr, Matrix, pbapply, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tidyr, withr
LinkingTo: Rcpp, rmio, bigstatsr
Suggests: batchelor, BiocStyle, bluster, knitr, magick, matrixStats, patchwork, RcppArmadillo, rmarkdown, scater, scran, Seurat, splatter, testthat (>= 3.0.0), UpSetR