scDiffCom
Differential Analysis of Intercellular Communication from scRNA-Seq Data
Description
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.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (1 non-OK)
dependencies in R code
Error in py_module_import(module, convert = convert) :
ModuleNotFoundError: No module named 'owlready2'
Run `reticulate::py_last_error()` for details.
Using Python: /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/3.9/bin/python3.9
Creating virtual environment 'r-owlready2' ...
Done!
Installing packages: pip, wheel, setuptools
Requirement already satisfied: pip in /Users/pkgbuild/.virtualenvs/r-owlready2/lib/python3.9/site-packages (21.2.4)
Collecting pip
Using cached pip-25.2-py3-none-any.whl (1.8 MB)
Collecting wheel
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Requirement already satisfied: setuptools in /Users/pkgbuild/.virtualenvs/r-owlready2/lib/python3.9/site-packages (58.0.4)
Collecting setuptools
Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
Installing collected packages: wheel, setuptools, pip
Attempting uninstall: setuptools
Found existing installation: setuptools 58.0.4
Uninstalling setuptools-58.0.4:
...[truncated]...
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 27.3/27.3 MB 3.8 MB/s 0:00:07
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: owlready2
Building wheel for owlready2 (pyproject.toml): started
Building wheel for owlready2 (pyproject.toml): finished with status 'done'
Created wheel for owlready2: filename=owlready2-0.48-cp39-cp39-macosx_11_0_universal2.whl size=23084262 sha256=5003cdf853da3e248914c7f9ae4bbcefcc629037538c6cd9acfa152a2c2e2ee8
Stored in directory: /Users/pkgbuild/Library/Caches/pip/wheels/70/6f/5c/2e8a43efa7697b1bd04085d4e8d97a82b19e4ee37c710a9f7b
Successfully built owlready2
Installing collected packages: owlready2
Successfully installed owlready2-0.48
Check History
NOTE 13 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
dependencies in R code
Error in py_module_import(module, convert = convert) : ModuleNotFoundError: No module named 'owlready2' Run `reticulate::py_last_error()` for details. Using Python: /Library/Developer/CommandLineTools/Library/Frameworks/Python3.framework/Versions/ ...[truncated]... 9acfa152a2c2e2ee8 Stored in directory: /Users/pkgbuild/Library/Caches/pip/wheels/70/6f/5c/2e8a43efa7697b1bd04085d4e8d97a82b19e4ee37c710a9f7b Successfully built owlready2 Installing collected packages: owlready2 Successfully installed owlready2-0.48