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spatial-communication
Analyze ligand-receptor interactions and cell-cell communication in spatial data. import squidpy as sq import scanpy as sc import pandas as pd import ...
spatial-deconvolution
Estimate cell type composition in spatial spots using scRNA-seq references. import scanpy as sc import anndata as ad import numpy as np import pandas ...
spatial-domains
Identify spatial domains and tissue regions by combining expression and spatial information. import squidpy as sq import scanpy as sc import numpy as ...
spatial-multiomics
| Platform | Resolution | Spots/Beads | Coverage | |----------|------------|-------------|----------| | Visium | 55 µm | 5,000 | Tissue-wide | | Visiu...
spatial-preprocessing
QC, filtering, normalization, and feature selection for spatial data. import squidpy as sq import scanpy as sc import numpy as np import matplotlib.py...
spatial-statistics
Compute spatial statistics and identify spatially variable features. import squidpy as sq import scanpy as sc import pandas as pd import numpy as np s...
tooluniverse-clinical-trial-matching
Transform patient molecular profiles and clinical characteristics into prioritized clinical trial recommendations. Searches ClinicalTrials.gov and cro...
pptx
| Task | Guide | |------|-------| | Read/analyze content | python -m markitdown presentation.pptx | | Edit or create from template | Read editing.md |...
tumor-clonal-evolution-agent
The Tumor Clonal Evolution Agent analyzes intratumoral heterogeneity (ITH), reconstructs tumor phylogenies, and tracks clonal dynamics over time. It i...
tpd-ternary-complex-agent
The TPD Ternary Complex Agent specializes in predicting and modeling ternary complex formation for targeted protein degradation (TPD). It uses AlphaFo...
immune-checkpoint-combination-agent
The Immune Checkpoint Combination Agent analyzes tumor molecular profiles to predict optimal immune checkpoint inhibitor (ICI) combinations. It integr...
bio-alignment-io
Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: Python: pip show <pac...