anglemania
This is the development version of anglemania; to use it, please install the devel version of Bioconductor.
Feature Extraction for scRNA-seq Dataset Integration
Bioconductor version: Development (3.22)
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")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | BatchEffect, FeatureExtraction, MultipleComparison, SingleCell, Software |
| Version | 0.99.6 |
| In Bioconductor since | BioC 3.22 (R-4.5) |
| 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_0.99.6.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |