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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 |
| 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: | 2024-09-30 |
| 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 |
| Reference manual: | SpaCCI.pdf |
| Package source: | SpaCCI_1.0.tar.gz |
| Windows binaries: | r-devel: SpaCCI_1.0.zip, r-release: SpaCCI_1.0.zip, r-oldrel: SpaCCI_1.0.zip |
| macOS binaries: | r-release (arm64): SpaCCI_1.0.tgz, r-oldrel (arm64): SpaCCI_1.0.tgz, r-release (x86_64): SpaCCI_1.0.tgz, r-oldrel (x86_64): SpaCCI_1.0.tgz |
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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.