Analysis tools to investigate changes in intercellular
communication from scRNA-seq data. Using a Seurat object as input,
the package infers which cell-cell interactions are present in the dataset
and how these interactions change between two conditions of interest
(e.g. young vs old). It relies on an internal database of ligand-receptor
interactions (available for human, mouse and rat) that have been gathered
from several published studies. Detection and differential analyses
rely on permutation tests. The package also contains several tools
to perform over-representation analysis and visualize the results. See
Lagger, C. et al. (2023) <doi:10.1038/s43587-023-00514-x> for a full
description of the methodology.
| Version: |
1.0.0 |
| Depends: |
R (≥ 4.0.0) |
| Imports: |
data.table, DelayedArray, future, future.apply, magrittr, methods, Seurat (≥ 4.0.0), stats, utils |
| Suggests: |
biomaRt, covr, DT, ggplot2, GOSemSim, igraph, kableExtra, KEGGREST, knitr, ontologyIndex, ontoProc, pkgdown, plotly, RColorBrewer, rmarkdown, rrvgo, spelling, shiny, shinythemes, shinyWidgets, SingleCellSignalR, testthat (≥ 3.0.0), visNetwork |
| Published: |
2023-11-03 |
| DOI: |
10.32614/CRAN.package.scDiffCom |
| Author: |
Cyril Lagger 
[aut, cre],
Eugen Ursu [aut],
Anais Equey [ctb] |
| Maintainer: |
Cyril Lagger <lagger.cyril at gmail.com> |
| License: |
MIT + file LICENSE |
| URL: |
https://cyrillagger.github.io/scDiffCom/ |
| NeedsCompilation: |
no |
| Language: |
en-US |
| Materials: |
README NEWS |
| CRAN checks: |
scDiffCom results |