anglemania
This is the released version of anglemania; for the devel version, see anglemania.
Feature Extraction for scRNA-seq Dataset Integration
Bioconductor version: Release (3.23)
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.
Author: Aaron Kollotzek [aut, cre]
, Vedran Franke [aut]
, Artem Baranovskii [aut], Altuna Akalin [aut], SFB1588 [fnd] (Funded by the DFG – Deutsche Forschungsgemeinschaft)
Maintainer: Aaron Kollotzek <aaron.kollotzek at mdc-berlin.de>
citation("anglemania")):
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("anglemania")
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("anglemania")| anglemania tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, FeatureExtraction, MultipleComparison, SingleCell, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | GPL (>= 3) |
| Depends | R (>= 4.5.0) |
| Imports | bigparallelr, bigstatsr, checkmate, digest, dplyr, Matrix, pbapply, S4Vectors, SingleCellExperiment, stats, SummarizedExperiment, tidyr, withr |
| System Requirements | |
| URL | https://github.com/BIMSBbioinfo/anglemania/ |
| Bug Reports | https://github.com/BIMSBbioinfo/anglemania/issues |
See More
| Suggests | batchelor, BiocStyle, bluster, knitr, magick, matrixStats, patchwork, RcppArmadillo, rmarkdown, scater, scran, Seurat, splatter, testthat (>= 3.0.0), UpSetR |
| Linking To | Rcpp, rmio, bigstatsr |
| 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 | anglemania_1.2.0.tar.gz |
| Windows Binary (x86_64) | anglemania_1.2.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | anglemania_1.2.0.tgz |
| macOS Binary (sonoma-arm64) | anglemania_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/anglemania |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/anglemania |
| Bioc Package Browser | https://code.bioconductor.org/browse/anglemania/ |
| Package Short Url | https://bioconductor.org/packages/anglemania/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |