Package: mumosa 1.15.0

Aaron Lun

mumosa: Multi-Modal Single-Cell Analysis Methods

Assorted utilities for multi-modal analyses of single-cell datasets. Includes functions to combine multiple modalities for downstream analysis, perform MNN-based batch correction across multiple modalities, and to compute correlations between assay values for different modalities.

Authors:Aaron Lun [aut, cre]

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mumosa.pdf |mumosa.html✨
mumosa/json (API)

# Install 'mumosa' in R:

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

On BioConductor:mumosa-1.13.2(bioc 3.20)mumosa-1.12.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology singlecell rnaseq

4.51 score 13 scripts 154 downloads 8 exports 75 dependencies

Last updated 23 days agofrom:df075a8ab5. Checks:OK: 4 NOTE: 2 ERROR: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	ERROR	Oct 31 2024

Exports:calculateMultiUMAP computeCorrelations findTopCorrelations intersectClusters intersectGraphs multiModalMNN rescaleByNeighbors runMultiUMAP

Dependencies:abind askpass assorthead batchelor beachmat BH Biobase BiocGenerics BiocNeighbors BiocParallel BiocSingular bluster cli cluster codetools cpp11 crayon curl DelayedArray DelayedMatrixStats dqrng edgeR FNN formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr igraph IRanges irlba jsonlite lambda.r lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats metapod mime openssl pkgconfig R6 Rcpp RcppAnnoy RcppEigen RcppProgress ResidualMatrix rlang RSpectra rsvd S4Arrays S4Vectors ScaledMatrix scran scuttle SingleCellExperiment sitmo snow SparseArray sparseMatrixStats statmod SummarizedExperiment sys UCSC.utils uwot vctrs XVector zlibbioc

Utilities for multi-modal single-cell analyses

Aaron Lun

Rendered fromoverview.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-03-05
Started: 2020-11-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Compute correlations between modes	computeCorrelations computeCorrelations,ANY-method computeCorrelations,SummarizedExperiment-method
Find top correlations between features	findTopCorrelations findTopCorrelations,ANY-method findTopCorrelations,SummarizedExperiment-method
Intersect pre-defined clusters	intersectClusters
Intersect two graphs	intersectGraphs
Multi-modal batch correction with MNNs	multiModalMNN
Rescale matrices for different modes	rescaleByNeighbors rescaleByNeighbors,ANY-method rescaleByNeighbors,SingleCellExperiment-method rescaleByNeighbors,SummarizedExperiment-method
Multi-modal UMAP	calculateMultiUMAP calculateMultiUMAP,ANY-method calculateMultiUMAP,SingleCellExperiment-method calculateMultiUMAP,SummarizedExperiment-method runMultiUMAP