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SpaCCI: Spatially Aware Cell-Cell Interaction Analysis

Provides tools for analyzing spatial cell-cell interactions based on ligand-receptor pairs, including functions for local, regional, and global analysis using spatial transcriptomics data. Integrates with databases like 'CellChat' <http://www.cellchat.org/>, 'CellPhoneDB' <https://www.cellphonedb.org/>, 'Cellinker' <https://www.rna-society.org/cellinker/>, 'ICELLNET' <https://github.com/soumelis-lab/ICELLNET>, and 'ConnectomeDB' <https://humanconnectome.org/software/connectomedb/> to identify ligand-receptor pairs, visualize interactions through heatmaps, chord diagrams, and infer interactions on different spatial scales.

Version: 1.0.2
Depends: R (≥ 3.5.0)
Imports: Rcpp (≥ 1.0.13), Seurat (≥ 4.0.0), nnls, ggrepel, pheatmap, circlize (≥ 0.4.12), Matrix, dplyr, patchwork, grDevices, reshape2, graphics, ggplot2
LinkingTo: Rcpp, RcppArmadillo
Published: 2024-10-24
DOI: 10.32614/CRAN.package.SpaCCI
Author: Li-Ting Ku [aut, cre]
Maintainer: Li-Ting Ku <lku at mdanderson.org>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
CRAN checks: SpaCCI results

Documentation:

Reference manual: SpaCCI.pdf

Downloads:

Package source: SpaCCI_1.0.2.tar.gz
Windows binaries: r-devel: SpaCCI_1.0.2.zip, r-release: SpaCCI_1.0.2.zip, r-oldrel: SpaCCI_1.0.2.zip
macOS binaries: r-release (arm64): SpaCCI_1.0.2.tgz, r-oldrel (arm64): SpaCCI_1.0.2.tgz, r-release (x86_64): SpaCCI_1.0.2.tgz, r-oldrel (x86_64): SpaCCI_1.0.2.tgz
Old sources: SpaCCI archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.