Package: blisa 1.0.0

Yunshun Chen

blisa: Infer Cell-Cell Communication from Spatial Transcriptomics

Identifies cell-cell communication hotspots in spatial transcriptomics data using bivariate Local Moran's I statistics on hexagonally binned cells. Provides functions for spatial weighting, ligand-receptor pair filtering, hotspot detection, and visualisation of sender-receiver cell-type interactions.

Authors:Yunshun Chen [aut, cre], Lei Qin [aut], Lizhong Chen [aut]

blisa_1.0.0.tar.gz
blisa_1.0.0.zip(r-4.7)blisa_1.0.0.zip(r-4.6)blisa_1.0.0.zip(r-4.5)
blisa_1.0.0.tgz(r-4.6-any)blisa_1.0.0.tgz(r-4.5-any)
blisa_1.0.0.tar.gz(r-4.7-any)blisa_1.0.0.tar.gz(r-4.6-any)
blisa_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
blisa/json (API)

# Install 'blisa' in R:

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

Bug tracker:https://github.com/chenlaboratory/blisa/issues

Pkgdown/docs site:https://chenlaboratory.github.io

On CRAN:

4.74 score 1 scripts 401 downloads 12 exports 98 dependencies

Last updated from:2a23260da7. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	202
source / vignettes	OK	250
linux-release-x86_64	OK	183
macos-release-arm64	OK	142
macos-oldrel-arm64	OK	139
windows-devel	OK	140
windows-release	OK	147
windows-oldrel	OK	146
wasm-release	OK	161

Exports:blisa computeSpatialWeights filterLRpairs hexBinCells is.blisa plotCCI plotCCILR plotCCIspatial plotCCIsummary plotHotspots plotLRrank runCCI

Dependencies:abind askpass Biobase BiocFileCache BiocGenerics bit bit64 blob boot cachem circlize class classInt cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl DBI dbplyr DelayedArray deldir digest doParallel dplyr e1071 farver fastLISA fastmap filelock foreach generics GenomicRanges GetoptLong ggplot2 GlobalOptions glue gtable httr2 IRanges isoband iterators KernSmooth labeling lattice lifecycle magick magrittr MASS Matrix MatrixGenerics matrixStats memoise openssl pillar pkgconfig png proxy purrr R6 rappdirs RColorBrewer Rcpp rjson rlang RSQLite s2 S4Arrays S4Vectors S7 scales Seqinfo sf shape SingleCellExperiment sp SparseArray SpatialExperiment spData spdep stringi stringr SummarizedExperiment sys tibble tidyr tidyselect units utf8 vctrs viridisLite withr wk XVector

Exploring cell-cell interaction with blisa

Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2026-07-09
Started: 2026-04-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
blisa: Bivariate Local Indicator of Spatial Association for spatial transcriptomics	blisa-package
Run BLISA spatial cell-cell communication analysis	blisa blisa.default blisa.SpatialExperiment
Compute Spatial Weights for BLISA	computeSpatialWeights
Filter ligand-receptor pairs by expression threshold	filterLRpairs
Bin cells into hexagonal spatial bins	hexBinCells
Test if an object is a blisa object	is.blisa
Heatmap of CCI scores across all ligand-receptor pairs	plotCCI plotCCI.blisa plotCCI.default
Sender-by-receiver heatmap of CCI scores for one ligand-receptor pair	plotCCILR plotCCILR.blisa plotCCILR.default
Spatial map of dominant sender-receiver cell-type pairs at BLISA hotspots	plotCCIspatial
Sender-by-receiver heatmap of aggregated CCI scores across LR pairs	plotCCIsummary plotCCIsummary.blisa plotCCIsummary.default
Spatial hotspot map for one ligand-receptor pair	plotHotspots plotHotspots.blisa
Dot plot ranking LR pairs by number of significant hotspot bins	plotLRrank plotLRrank.blisa plotLRrank.data.frame
Score cell-cell interactions from BLISA hotspots	runCCI runCCI.blisa runCCI.default