Package: cellchatr 0.99.1

Mayank Gandhi

cellchatr: Fast Ligand-Receptor Interaction Screening for Single-Cell Data Using Rust

Fast identification of over-expressed genes and ligand-receptor interactions in single-cell RNA-seq data, the pre-processing steps of cell-cell communication analysis tools such as CellChat. Works directly on SummarizedExperiment and SingleCellExperiment objects and accepts any ligand-receptor table (for example the CellChatDB interaction table). The per-gene, per-cell-group Wilcoxon rank-sum tests are implemented in Rust via extendr and run in parallel with Rayon.

Authors:Mayank Gandhi [aut, cre]

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cellchatr_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cellchatr/json (API)

# Install 'cellchatr' in R:

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

Bug tracker:https://github.com/mayankgandhi13/cellchatr/issues

On CRAN:

singlecell geneexpression transcriptomics differentialexpression network software rust cargo

3.40 score 6 exports 17 dependencies

Last updated from:e315f0b33c. Checks:1 NOTE, 15 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	293
linux-devel-arm64	OK	203
linux-devel-x86_64	OK	354
source / vignettes	OK	308
linux-release-arm64	OK	311
linux-release-x86_64	OK	242
macos-release-arm64	OK	272
macos-release-x86_64	OK	534
macos-oldrel-arm64	OK	190
macos-oldrel-x86_64	OK	620
windows-devel-arm64	OK	448
windows-devel-x86_64	OK	261
windows-release-arm64	OK	347
windows-release-x86_64	OK	234
windows-oldrel-x86_64	OK	212
wasm-release	OK	156

Exports:findOverexpressedGenes identifyInteractions matchLRPairs rust_match_lr_pairs rust_subset_genes rust_wilcoxon_filter

Dependencies:abind Biobase BiocGenerics DelayedArray generics GenomicRanges IRanges lattice Matrix MatrixGenerics matrixStats S4Arrays S4Vectors Seqinfo SparseArray SummarizedExperiment XVector

cellchatr: fast ligand-receptor pre-filtering for single-cell data

Rendered fromcellchatr-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-10-01
Started: 2026-05-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Find over-expressed genes per cell group	findOverexpressedGenes findOverexpressedGenes,ANY-method findOverexpressedGenes,SummarizedExperiment-method
Identify over-expressed ligand-receptor interactions	identifyInteractions
Match genes to ligand-receptor interactions	matchLRPairs
Match overexpressed genes against CellChatDB ligand-receptor pairs.	rust_match_lr_pairs
Filter expression matrix genes to only those present in CellChatDB.	rust_subset_genes
Identify over-expressed genes per cell type using Wilcoxon rank-sum test.	rust_wilcoxon_filter