Package: mumosa 1.21.0

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]

mumosa_1.21.0.tar.gz
mumosa_1.21.0.zip(r-4.7)mumosa_1.21.0.zip(r-4.6)mumosa_1.21.0.zip(r-4.5)
mumosa_1.21.0.tgz(r-4.6-any)mumosa_1.21.0.tgz(r-4.5-any)
mumosa_1.21.0.tar.gz(r-4.7-any)mumosa_1.21.0.tar.gz(r-4.6-any)
mumosa_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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-1.21.0(bioc 3.24)mumosa-1.20.0(bioc 3.23)

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

immunooncology singlecell rnaseq

4.38 score 16 scripts 344 downloads 8 exports 64 dependencies

Last updated from:cf328e4af1. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	405
linux-devel-x86_64	WARNING	504
source / vignettes	OK	405
linux-release-x86_64	WARNING	532
macos-release-arm64	WARNING	315
macos-oldrel-arm64	WARNING	290
windows-devel	WARNING	896
windows-release	WARNING	997
windows-oldrel	WARNING	863
wasm-release	OK	574

Exports:calculateMultiUMAP computeCorrelations findTopCorrelations intersectClusters intersectGraphs multiModalMNN rescaleByNeighbors runMultiUMAP

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

Utilities for multi-modal single-cell analyses

Rendered fromoverview.Rmdusingknitr::rmarkdown

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