PACE
A hierarchical empirical Bayes framework for proximity-associated changes in expression — how a cell's gene
expression shifts near specific neighbouring cell types — in imaging-based spatial transcriptomics (Xenium, CosMx).
Overview
PACE quantifies how proximity to specific neighbouring cell types reshapes a cell's gene expression. It fits
hierarchical negative binomial mixed models with partial pooling across cell types, corrects for transcript
contamination between adjacent cells with a per-cell ambient term, and decomposes expression variance into
cell-type identity, spatial cell state, contamination, and residual components. A per-gene driver score
ranks the genes that mediate each focal–neighbour relationship.
Input and output follow AnnData conventions:
a single call to pace_fit() returns a PaceFit object, read out with neighbour_slopes(),
variance_decomposition(), and top_drivers(). See examples/demo.py for a worked breast cancer example and
docs/usage.md for the readouts and options in full.
import pace
fit = pace.pace_fit(adata, cell_type="cell_type")
pace.top_drivers(fit, "Macrophage", "Tumour").to_dataframe().head()
This is the Python implementation. PACE is also an R/Bioconductor package; both compile the same C++ core, so a fit is the same fit in either language.
Installation
PACE requires a C++ compiler and Eigen 3.4 for the contamination-correcting solver. Installing a released
wheel avoids both.
pip install pace-spatial
For the development version:
pip install "git+https://github.com/ecool50/pace-python"
Building from source needs Eigen 3.4 specifically — later majors reduce in a different order and move the fitted
effects — and, on macOS, Apple's toolchain rather than a conda or Homebrew clang:
bash tools/fetch_eigen.sh
EIGEN_INCLUDE_DIR=$PWD/eigen-3.4.0 CC=/usr/bin/clang CXX=/usr/bin/clang++ \
LDSHARED="/usr/bin/clang -bundle -undefined dynamic_lookup" pip install -e ".[all]"
Submitting an issue or feature request
PACE is still under active development. We would greatly appreciate any and
all feedback related to the package.
- Python package related issues should be raised here.
- For general questions and feedback, please contact us directly via ewil3501@uni.sydney.edu.au.
Author
- Elijah Willie
- Shreya Rajesh Rao
- John Ormerod
- Ellis Patrick - @TheEllisPatrick
1 maintainer
Metadata
1 maintainer
Release files for pace-spatial 0.1.0
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Transparency logRelease files / pace_spatial-0.1.0-cp39-cp39-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
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| Tags | CPython 3.9 Linux glibc 2.24+ ARM64 Linux glibc 2.28+ ARM64 |
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Transparency logRelease files / pace_spatial-0.1.0-cp39-cp39-macosx_11_0_x86_64.whl
| Download URL | pace_spatial-0.1.0-cp39-cp39-macosx_11_0_x86_64.whl |
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Transparency logRelease files / pace_spatial-0.1.0-cp39-cp39-macosx_11_0_arm64.whl
| Download URL | pace_spatial-0.1.0-cp39-cp39-macosx_11_0_arm64.whl |
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| Size | 470.1 kB |
| Tags | CPython 3.9 macOS 11.0+ ARM64 |
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