Package: anglemania 1.3.0

Aaron Kollotzek

anglemania: Feature Extraction for scRNA-seq Dataset Integration

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.

Authors:Aaron Kollotzek [aut, cre], Vedran Franke [aut], Artem Baranovskii [aut], Altuna Akalin [aut], SFB1588 [fnd]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
anglemania/json (API)

# Install 'anglemania' in R:

install.packages('anglemania', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bimsbbioinfo/anglemania/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:anglemania-1.3.0(bioc 3.24)anglemania-1.2.0(bioc 3.23)

singlecell batcheffect multiplecomparison featureextraction cpp

5.51 score 4 stars 2 scripts 23 exports 69 dependencies

Last updated from:097e32809c. Checks:12 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	351
linux-devel-arm64	NOTE	351
linux-devel-x86_64	NOTE	391
source / vignettes	OK	527
linux-release-arm64	NOTE	362
linux-release-x86_64	NOTE	489
macos-release-arm64	NOTE	186
macos-release-x86_64	NOTE	994
macos-oldrel-arm64	NOTE	179
macos-oldrel-x86_64	NOTE	512
windows-devel	NOTE	285
windows-release	NOTE	270
windows-oldrel	NOTE	248
wasm-release	OK	227

Exports:add_unique_batch_key anglemania big_cor_no_warning big_crossprodSelf_no_warning big_mat_list_mean big_scale_no_warning check_params CutBySize extract_angles extract_rows_for_unique_genes factorise get_anglemania_genes get_anglemania_stats_df get_dstat get_intersect_genes get_list_stats normalize_matrix permute_nonzero prefilter_angl replace_with_na sce_example select_genes sparse_to_fbm

Dependencies:abind backports bigassertr bigparallelr bigstatsr Biobase BiocGenerics bit checkmate cli codetools cowplot cpp11 DelayedArray digest doParallel dplyr farver ff flock foreach generics GenomicRanges ggplot2 glue gtable IRanges isoband iterators labeling lattice lifecycle magrittr Matrix MatrixGenerics matrixStats parallelly pbapply pillar pkgconfig ps purrr R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RhpcBLASctl rlang rmio RSpectra S4Arrays S4Vectors S7 scales Seqinfo SingleCellExperiment SparseArray stringi stringr SummarizedExperiment tibble tidyr tidyselect utf8 vctrs viridisLite withr XVector

anglemania Tutorial

Rendered fromanglemania_tutorial.Rmdusingknitr::rmarkdown

Last update: 2025-10-14
Started: 2024-11-15

Help page	Topics
anglemania	add_unique_batch_key anglemania check_params get_intersect_genes
Calculate cosine angle between genes	extract_angles
Factorize Angle Matrices into Z-Scores	factorise
permute non-zero elements of vectors	permute_nonzero
Generate example SingleCellExperiment object	sce_example

Package: anglemania 1.3.0

anglemania: Feature Extraction for scRNA-seq Dataset Integration

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Usage by other packages (reverse dependencies)