@bgicli/bgicli 2.1.1 → 2.2.0

package/data/skills/slurm-job-script-generator/SKILL.md

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+---
+name: slurm-job-script-generator
+description: Generate SLURM `sbatch` job scripts and sanity-check HPC resource requests (nodes, tasks, CPUs, memory, GPUs) for simulation runs. Use when preparing submission scripts, deciding MPI vs MPI+OpenMP layouts, standardizing `#SBATCH` directives, or debugging job launch configuration (`sbatch`/`srun`).
+allowed-tools: Read, Bash, Write, Grep, Glob
+---
+
+# SLURM Job Script Generator
+
+## Goal
+
+Generate a correct, copy-pasteable SLURM job script (`.sbatch`) for running a simulation, and surface common configuration mistakes (bad walltime format, conflicting memory flags, oversubscription hints).
+
+## Requirements
+
+- Python 3.8+
+- No external dependencies (Python standard library only)
+- Works on Linux, macOS, and Windows (script generation only)
+
+## Inputs to Gather
+
+| Input | Description | Example |
+|-------|-------------|---------|
+| Job name | Short identifier for the job | `phasefield-strong-scaling` |
+| Walltime | SLURM time limit | `00:30:00` |
+| Partition | Cluster partition/queue (if required) | `compute` |
+| Account | Project/account (if required) | `matsim` |
+| Nodes | Number of nodes to allocate | `2` |
+| MPI tasks | Total tasks, or tasks per node | `128` or `64` per node |
+| Threads | CPUs per task (OpenMP threads) | `2` |
+| Memory | `--mem` or `--mem-per-cpu` (cluster policy dependent) | `32G` |
+| GPUs | GPUs per node (optional) | `4` |
+| Working directory | Where the run should execute | `$SLURM_SUBMIT_DIR` |
+| Modules | Environment modules to load (optional) | `gcc/12`, `openmpi/4.1` |
+| Run command | The command to launch under SLURM | `./simulate --config cfg.json` |
+
+## Decision Guidance
+
+### MPI vs MPI+OpenMP layout
+
+```
+Does the code use OpenMP / threading?
+├── NO  → Use MPI-only: cpus-per-task=1
+└── YES → Use hybrid: set cpus-per-task = threads per MPI rank
+          and export OMP_NUM_THREADS = cpus-per-task
+```
+
+**Rule of thumb:** if you see diminishing strong-scaling efficiency at high MPI ranks, try fewer ranks with more threads per rank (and measure).
+
+### Memory flag selection
+
+- Use **either** `--mem` (per node) **or** `--mem-per-cpu` (per CPU), not both.
+- Follow your cluster’s documentation; some sites enforce one style.
+- SLURM `--mem` units are integer MB by default, or an integer with suffix `K/M/G/T` (and `--mem=0` commonly means “all memory on node”).
+
+## Script Outputs (JSON Fields)
+
+| Script | Key Outputs |
+|--------|-------------|
+| `scripts/slurm_script_generator.py` | `results.script`, `results.directives`, `results.derived`, `results.warnings` |
+
+## Workflow
+
+1. Gather cluster constraints (partition/account, GPU policy, memory policy).
+2. Choose a process layout (MPI-only vs hybrid MPI+OpenMP).
+3. Generate the script with `slurm_script_generator.py`.
+4. Inspect warnings (conflicts, suspicious layouts).
+5. Save the generated script as `job.sbatch`.
+6. Submit with `sbatch job.sbatch` and monitor with `squeue`.
+
+## CLI Examples
+
+```bash
+# Preview a job script (prints to stdout)
+python3 skills/hpc-deployment/slurm-job-script-generator/scripts/slurm_script_generator.py \
+  --job-name phasefield \
+  --time 00:10:00 \
+  --partition compute \
+  --nodes 1 \
+  --ntasks-per-node 8 \
+  --cpus-per-task 2 \
+  --mem 16G \
+  --module gcc/12 \
+  --module openmpi/4.1 \
+  -- \
+  ./simulate --config config.json
+
+# Write to a file and also emit structured JSON
+python3 skills/hpc-deployment/slurm-job-script-generator/scripts/slurm_script_generator.py \
+  --job-name phasefield \
+  --time 00:10:00 \
+  --nodes 1 \
+  --ntasks 16 \
+  --cpus-per-task 1 \
+  --out job.sbatch \
+  --json \
+  -- \
+  /bin/echo hello
+```
+
+## Conversational Workflow Example
+
+**User**: I need an `sbatch` script for my MPI simulation. I want 2 nodes, 64 ranks per node, 2 OpenMP threads per rank, and 2 hours.
+
+**Agent workflow**:
+1. Confirm partition/account and whether GPUs are needed.
+2. Generate a hybrid job script:
+   ```bash
+   python3 scripts/slurm_script_generator.py --job-name run --time 02:00:00 --nodes 2 --ntasks-per-node 64 --cpus-per-task 2 -- -- ./simulate
+   ```
+3. Explain the mapping:
+   - Total ranks = 128
+   - Threads per rank = 2 (`OMP_NUM_THREADS=2`)
+4. If the user provides node core counts, sanity-check oversubscription using `--cores-per-node`.
+
+## Error Handling
+
+| Error | Cause | Resolution |
+|-------|-------|------------|
+| `time must be HH:MM:SS or D-HH:MM:SS` | Bad walltime format | Use `00:30:00` or `1-00:00:00` |
+| `nodes must be positive` | Non-positive nodes | Provide `--nodes >= 1` |
+| `Provide either --mem or --mem-per-cpu, not both` | Conflicting memory directives | Choose one memory style |
+| `Provide a run command after --` | Missing launch command | Add `-- ./simulate ...` |
+
+## Limitations
+
+- Does not query cluster hardware or site policies; it can only validate internal consistency.
+- SLURM installations vary (GPU directives, QoS rules, partitions). Adjust directives for your site.
+
+## References
+
+- `references/slurm_directives.md` - Common `#SBATCH` directives and mapping tips
+
+## Version History
+
+- **v1.0.0** (2026-02-25): Initial SLURM job script generator

package/data/skills/solublempnn/SKILL.md

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+---
+name: solublempnn
+description: >
+  Solubility-optimized protein sequence design using SolubleMPNN.
+  Use this skill when: (1) Designing for E. coli expression,
+  (2) Optimizing solubility of designed proteins,
+  (3) Reducing aggregation propensity,
+  (4) Need high-yield expression,
+  (5) Avoiding inclusion body formation.
+
+  For standard design, use proteinmpnn.
+  For ligand-aware design, use ligandmpnn.
+license: MIT
+category: design-tools
+tags: [sequence-design, inverse-folding, solubility]
+biomodals_script: modal_ligandmpnn.py
+---
+
+# SolubleMPNN Solubility-Optimized Design
+
+## Prerequisites
+
+| Requirement | Minimum | Recommended |
+|-------------|---------|-------------|
+| Python | 3.8+ | 3.10 |
+| CUDA | 11.0+ | 11.7+ |
+| GPU VRAM | 8GB | 16GB (T4) |
+| RAM | 8GB | 16GB |
+
+## How to run
+
+> **First time?** See [Installation Guide](../../docs/installation.md) to set up Modal and biomodals.
+
+### Option 1: Modal (recommended)
+SolubleMPNN uses the ProteinMPNN Modal wrapper with soluble model:
+```bash
+cd biomodals
+modal run modal_proteinmpnn.py \
+  --pdb-path backbone.pdb \
+  --num-seq-per-target 16 \
+  --sampling-temp 0.1 \
+  --model-name v_48_020
+```
+
+**GPU**: T4 (16GB) | **Timeout**: 600s default
+
+### Option 2: Local installation
+```bash
+git clone https://github.com/dauparas/ProteinMPNN.git
+cd ProteinMPNN
+
+# Use soluble model weights
+python protein_mpnn_run.py \
+  --pdb_path backbone.pdb \
+  --out_folder output/ \
+  --num_seq_per_target 16 \
+  --sampling_temp "0.1" \
+  --model_name "v_48_020"  # Soluble model
+```
+
+## Key parameters
+
+| Parameter | Default | Range | Description |
+|-----------|---------|-------|-------------|
+| `--pdb_path` | required | path | Input structure |
+| `--num_seq_per_target` | 1 | 1-1000 | Sequences per structure |
+| `--sampling_temp` | "0.1" | "0.0001-1.0" | Temperature (string!) |
+| `--model_name` | v_48_020 | string | Soluble model variant |
+
+## Model Variants
+
+| Model | Description | Use Case |
+|-------|-------------|----------|
+| v_48_002 | Standard | General design |
+| v_48_020 | Soluble-trained | E. coli expression |
+| v_48_030 | High solubility | Difficult targets |
+
+## Output format
+
+```
+output/
+├── seqs/backbone.fa
+└── backbone_pdb/backbone_0001.pdb
+```
+
+## Sample output
+
+### Successful run
+```
+$ python protein_mpnn_run.py --pdb_path backbone.pdb --model_name v_48_020 --num_seq_per_target 8
+Loading soluble model weights (v_48_020)...
+Designing sequences for backbone.pdb
+Generated 8 sequences in 2.1 seconds
+
+output/seqs/backbone.fa:
+>backbone_0001, score=1.31, global_score=1.24, seq_recovery=0.78
+MKTAYIAKQRQISFVKSHFSRQLE...
+>backbone_0002, score=1.28, global_score=1.21, seq_recovery=0.81
+MKTAYIAKQRQISFVKSQFSRQLD...
+```
+
+**What good output looks like:**
+- Score: 1.0-2.0 (lower = more confident)
+- Reduced hydrophobic patches compared to standard MPNN
+- Improved charge distribution
+
+## Decision tree
+
+```
+Should I use SolubleMPNN?
+│
+├─ What expression system?
+│  ├─ E. coli → SolubleMPNN ✓
+│  ├─ Mammalian → ProteinMPNN (PTMs matter more)
+│  └─ Yeast → Either
+│
+├─ History of expression problems?
+│  ├─ Yes, aggregation → SolubleMPNN ✓
+│  ├─ Yes, low yield → SolubleMPNN ✓
+│  └─ No → ProteinMPNN is fine
+│
+├─ What's in the binding site?
+│  ├─ Small molecule / ligand → Use LigandMPNN
+│  └─ Nothing / protein only → SolubleMPNN ✓
+│
+└─ Need highest solubility?
+   ├─ Yes → Use v_48_030 model
+   └─ Standard → Use v_48_020 model
+```
+
+## Typical performance
+
+| Campaign Size | Time (T4) | Cost (Modal) | Notes |
+|---------------|-----------|--------------|-------|
+| 100 backbones × 8 seq | 15-20 min | ~$2 | Standard |
+| 500 backbones × 8 seq | 1-1.5h | ~$8 | Large campaign |
+
+**Expected improvement**: +15-30% solubility score vs standard ProteinMPNN.
+
+---
+
+## Verify
+
+```bash
+grep -c "^>" output/seqs/*.fa  # Should match backbone_count × num_seq_per_target
+```
+
+---
+
+## Troubleshooting
+
+**Still insoluble**: Try v_48_030 (higher solubility bias)
+**Low diversity**: Increase temperature to 0.2
+**Poor folding**: Use standard ProteinMPNN and optimize later
+
+### Error interpretation
+
+| Error | Cause | Fix |
+|-------|-------|-----|
+| `RuntimeError: CUDA out of memory` | Long protein or large batch | Reduce batch_size |
+| `FileNotFoundError: v_48_020` | Missing model weights | Download soluble weights |
+
+---
+
+**Next**: Structure prediction for validation → `protein-qc` for filtering.

package/data/skills/spatial-agent/SKILL.md

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+<!--
+# COPYRIGHT NOTICE
+# This file is part of the "Universal Biomedical Skills" project.
+# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
+# All Rights Reserved.
+#
+# This code is proprietary and confidential.
+# Unauthorized copying of this file, via any medium is strictly prohibited.
+#
+# Provenance: Authenticated by MD BABU MIA
+
+-->
+
+---
+name: 'spatial-agent'
+description: 'An agent that interprets spatial transcriptomics data to propose mechanistic hypotheses and analyze tissue organization.'
+measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
+allowed-tools:
+  - read_file
+  - run_shell_command
+---
+
+
+# SpatialAgent
+
+SpatialAgent focuses on the biological interpretation of spatial transcriptomics data, specifically aiming to propose mechanistic hypotheses about tissue organization and cellular interactions.
+
+## When to Use This Skill
+
+*   **Mechanistic Interpretation**: When you have clusters or spatial domains and need to understand *why* they are organized that way.
+*   **Cell-Cell Interaction**: To predict and interpret ligand-receptor interactions in a spatial context.
+*   **Hypothesis Generation**: To propose biological mechanisms driving the observed spatial heterogeneity.
+
+## Core Capabilities
+
+1.  **Tissue Organization Analysis**: Decodes the structural logic of tissues (e.g., layers, niches).
+2.  **Cellular Interaction Prediction**: Identifies potential signaling pathways active at domain boundaries.
+3.  **Hypothesis Proposal**: Generates testable biological hypotheses based on spatial data.
+
+## Workflow
+
+1.  **Input Analysis**: Accepts processed ST data (e.g., cluster annotations, DEG lists per spatial domain).
+2.  **Knowledge Retrieval**: Queries biological knowledge bases regarding the observed cell types and genes.
+3.  **Synthesis**: Constructs a narrative explaining the spatial arrangement (e.g., "The proximity of fibroblasts and tumor cells suggests a desmoplastic reaction mediated by TGF-beta signaling...").
+
+## Example Usage
+
+**User**: "Why are the macrophages located at the boundary of the tumor core in this sample?"
+
+**Agent Action**:
+1.  Analyzes the gene expression of macrophages and adjacent tumor cells.
+2.  Checks for ligand-receptor pairs (e.g., CSF1-CSF1R).
+3.  Proposes: "Macrophages are likely recruited by CSF1 secreted by the tumor cells, forming an immunosuppressive barrier..."
+
+
+<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

package/data/skills/spatial-epigenomics-agent/SKILL.md

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+<!--
+# COPYRIGHT NOTICE
+# This file is part of the "Universal Biomedical Skills" project.
+# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
+# All Rights Reserved.
+#
+# This code is proprietary and confidential.
+# Unauthorized copying of this file, via any medium is strictly prohibited.
+#
+# Provenance: Authenticated by MD BABU MIA
+
+-->
+
+---
+name: 'spatial-epigenomics-agent'
+description: 'AI-powered spatial epigenomics analysis combining chromatin accessibility, histone modifications, and DNA methylation with spatial coordinates for tissue architecture mapping.'
+measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
+allowed-tools:
+  - read_file
+  - run_shell_command
+---
+
+
+# Spatial Epigenomics Agent
+
+The **Spatial Epigenomics Agent** analyzes spatial epigenomic data combining chromatin accessibility (ATAC-seq), histone modifications (CUT&Tag), and DNA methylation with spatial coordinates. It maps regulatory landscapes across tissue architecture to understand cell-state regulation in spatial context.
+
+## When to Use This Skill
+
+* When analyzing spatial ATAC-seq data (Slide-seq + ATAC, DBiT-seq).
+* To map chromatin accessibility across tissue microenvironments.
+* For spatial profiling of histone modifications (H3K27ac, H3K4me3, H3K27me3).
+* When integrating spatial epigenomics with spatial transcriptomics.
+* To identify spatially-variable regulatory elements and enhancers.
+
+## Core Capabilities
+
+1. **Spatial ATAC Analysis**: Process spatial chromatin accessibility data to identify open chromatin regions with spatial coordinates.
+
+2. **Spatial CUT&Tag**: Analyze spatially-resolved histone modification profiles (H3K27ac for enhancers, H3K4me3 for promoters).
+
+3. **Spatial Methylation**: Map DNA methylation patterns across tissue sections using spatial bisulfite methods.
+
+4. **Multi-Modal Integration**: Combine spatial epigenomics with spatial transcriptomics for regulatory network inference.
+
+5. **Regulatory Element Mapping**: Identify spatially-variable enhancers, promoters, and silencers.
+
+6. **3D Chromatin Organization**: Integrate with MERFISH/seqFISH+ for spatial chromatin organization.
+
+## Technologies Supported
+
+| Technology | Epigenetic Mark | Resolution | Method |
+|------------|-----------------|------------|--------|
+| Spatial-ATAC-seq | Open chromatin | ~10-50μm | Microfluidic barcoding |
+| DBiT-seq | ATAC + expression | ~10μm | Deterministic barcoding |
+| Spatial-CUT&Tag | Histone marks | ~50μm | Cleavage under targets |
+| Spatial-MethylSeq | DNA methylation | Variable | Bisulfite conversion |
+| MERFISH + epigenetics | 3D organization | Single-cell | Imaging-based |
+
+## Workflow
+
+1. **Input**: Spatial epigenomics data (BAM files + spatial coordinates) or processed peak matrices.
+
+2. **Preprocessing**: Alignment, deduplication, peak calling with spatial awareness.
+
+3. **Spatial Clustering**: Identify spatial domains with similar epigenetic profiles.
+
+4. **Peak Annotation**: Map peaks to genomic features (promoters, enhancers, gene bodies).
+
+5. **Motif Analysis**: Identify transcription factor binding motifs in spatially-variable peaks.
+
+6. **Integration**: Combine with expression data for regulatory inference.
+
+7. **Output**: Spatial peak maps, regulatory networks, domain annotations.
+
+## Example Usage
+
+**User**: "Analyze this spatial ATAC-seq dataset to identify spatially-variable regulatory elements in the tumor microenvironment."
+
+**Agent Action**:
+```bash
+python3 Skills/Genomics/Spatial_Epigenomics_Agent/spatial_epigenomics.py \
+    --input spatial_atac_fragments.tsv.gz \
+    --coordinates spot_coordinates.csv \
+    --peaks macs2_peaks.bed \
+    --spatial_variable true \
+    --motif_db jaspar_2024 \
+    --integrate_with spatial_rna.h5ad \
+    --output spatial_epi_results/
+```
+
+## Analysis Modules
+
+**1. Spatial Peak Calling**
+- Adapted MACS2/Genrich for spatial data
+- Spatial autocorrelation of accessibility
+- Pseudo-bulk and single-spot approaches
+
+**2. Spatial Domain Detection**
+- Graph-based clustering (Leiden, Louvain)
+- Hidden Markov Random Fields
+- Deep learning segmentation
+
+**3. Transcription Factor Analysis**
+- ChromVAR for TF activity scores
+- SCENIC+ for spatial regulon inference
+- Motif enrichment in spatial domains
+
+**4. Enhancer-Gene Linking**
+- Activity-by-contact (ABC) model adaptation
+- Spatial correlation of enhancer accessibility with gene expression
+- Chromatin loop integration
+
+## Integration with Spatial Transcriptomics
+
+```
+Spatial ATAC-seq          Spatial RNA-seq
+      |                        |
+      v                        v
+  Peak Matrix            Expression Matrix
+      |                        |
+      +--------> Integration <-+
+                     |
+                     v
+         Regulatory Network
+         (Enhancer -> TF -> Gene)
+```
+
+## Key Metrics
+
+| Metric | Description | Typical Range |
+|--------|-------------|---------------|
+| TSS Enrichment | Signal at transcription start sites | >4 good quality |
+| FRiP | Fraction reads in peaks | >30% |
+| Spatial autocorrelation | Moran's I for epigenetic features | 0.2-0.8 |
+| Spots per gene | Detection sensitivity | 100-500 |
+
+## Prerequisites
+
+* Python 3.10+
+* SnapATAC2, ArchR for ATAC analysis
+* Squidpy, Scanpy for spatial analysis
+* MACS2/Genrich for peak calling
+
+## Related Skills
+
+* Spatial_Transcriptomics - For gene expression spatial mapping
+* Epigenomics_MethylGPT_Agent - For methylation analysis
+* Single_Cell - For non-spatial epigenomics
+
+## Applications
+
+1. **Tumor Microenvironment**: Map regulatory programs across tumor-stroma boundary
+2. **Development**: Track enhancer activation during tissue morphogenesis
+3. **Neuroanatomy**: Brain region-specific regulatory landscapes
+4. **Disease Mechanisms**: Spatial dysregulation in pathology
+
+## Author
+
+AI Group - Biomedical AI Platform
+
+
+<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

package/data/skills/spatial-transcriptomics-agent/SKILL.md

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+<!--
+# COPYRIGHT NOTICE
+# This file is part of the "Universal Biomedical Skills" project.
+# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
+# All Rights Reserved.
+#
+# This code is proprietary and confidential.
+# Unauthorized copying of this file, via any medium is strictly prohibited.
+#
+# Provenance: Authenticated by MD BABU MIA
+
+-->
+
+---
+name: spatial-transcriptomics-agent
+description: Spatial analyst
+keywords:
+  - spatial
+  - h5ad
+  - H&E
+  - clustering
+  - SVG
+measurable_outcome: For each sample, deliver ≥1 spatial domain map + SVG list + narrative interpretation within 30 minutes.
+license: MIT
+metadata:
+  author: LiuLab
+  version: "1.0.0"
+compatibility:
+  - system: Python 3.9+
+allowed-tools:
+  - run_shell_command
+  - read_file
+  - web_fetch
+---
+
+# Spatial Transcriptomics Agent
+
+Run STAgent to align histology images with expression matrices, perform clustering/SVG detection, and generate literature-backed spatial reports.
+
+## When to Use
+- Analysis of Visium/Xenium or similar ST datasets.
+- Visual reasoning over spatial plots, H&E images, or cluster maps.
+- Automatically generating Scanpy/Squidpy code for new ST workflows.
+- Hypothesis generation about spatial gene expression patterns.
+
+## Core Capabilities
+1. **Dynamic code generation:** Create/execute Python scripts for QC, clustering, SVG detection.
+2. **Visual reasoning:** Interpret spatial plots to identify tissue domains and cell neighborhoods.
+3. **Literature retrieval:** Pull references that contextualize findings.
+4. **Report generation:** Deliver publication-style writeups with plots and SVG tables.
+
+## Workflow
+1. **Env setup:** `conda env create -f environment.yml && conda activate STAgent`.
+2. **Data prep:** Supply `expression_path` (`.h5ad`/Spaceranger) + `image_path` (H&E/IF) and metadata.
+3. **Task selection:** Choose tasks such as `cluster`, `find_svg`, `annotate_domains`, or composite instructions; run `python repo/src/main.py --data_path ... --task "..."`.
+4. **Execute & interpret:** Let STAgent generate scripts, run analyses, and interpret results with literature references.
+5. **Package outputs:** Save UMAP/spatial plots, SVG tables, QC details, and summary markdown.
+
+## Example Usage
+```text
+User: "Analyze this breast cancer ST dataset, find immune infiltrates."
+Agent: loads data, runs `sqidpy.gr.spatial_neighbors`, computes Leiden clusters, plots marker genes (CD3D, CD19), and summarizes which clusters map to tumor core vs. stromal/immune zones.
+```
+
+## Guardrails
+- Document coordinate systems and any scaling between imaging and expression coordinates.
+- Avoid definitive cell-type labels without supporting markers.
+- Capture QC parameters for reproducibility.
+
+## References
+- Source repo: https://github.com/LiuLab-Bioelectronics-Harvard/STAgent
+- See local `README.md` for detailed instructions.
+
+
+<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->

package/data/skills/spatial-transcriptomics-analysis/SKILL.md

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+<!--
+# COPYRIGHT NOTICE
+# This file is part of the "Universal Biomedical Skills" project.
+# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
+# All Rights Reserved.
+#
+# This code is proprietary and confidential.
+# Unauthorized copying of this file, via any medium is strictly prohibited.
+#
+# Provenance: Authenticated by MD BABU MIA
+
+-->
+
+---
+name: spatial-transcriptomics-analysis
+description: Automated analysis pipeline for Spatial Transcriptomics (Visium, Xenium) integrating histology and gene expression.
+keywords:
+  - spatial-transcriptomics
+  - visium
+  - xenium
+  - scanpy
+  - squidpy
+measurable_outcome: Process a Visium dataset, identify spatially variable genes, and generate spatial feature plots within 30 minutes.
+license: MIT
+metadata:
+  author: MD BABU MIA, PhD
+  version: "1.0.0"
+compatibility:
+  - system: python 3.9+
+allowed-tools:
+  - run_shell_command
+  - read_file
+  - write_file
+---
+
+# Spatial Transcriptomics Skill
+
+**Version:** 1.0.0
+**Author:** MD BABU MIA, PhD
+**Date:** February 2026
+
+## Overview
+This skill provides automated analysis capabilities for Spatial Transcriptomics data, specifically designed for 10x Visium and Xenium platforms. It enables the integration of histological data with gene expression profiles to uncover spatial organization of cell types.
+
+## Capabilities
+1.  **Data Loading:** Supports Spaceranger output (h5, images).
+2.  **QC & Preprocessing:** Spatial QC metrics, normalization.
+3.  **Spatial Variable Features:** Identification of spatially variable genes (SVGs) using Moran's I and Geary's C.
+4.  **Deconvolution:** Interface for cell type deconvolution (mapping scRNA-seq to spatial).
+5.  **Visualization:** Interactive spatial plots overlaying gene expression on tissue images.
+
+## Usage
+```python
+from Skills.Genomics.Spatial_Transcriptomics.spatial_analyzer import SpatialAnalyzer
+
+# Initialize
+sa = SpatialAnalyzer(data_path="./data/visium_sample1")
+
+# Run Pipeline
+sa.load_data()
+sa.preprocess()
+sa.find_spatial_features()
+sa.plot_spatial("INS", save_path="./output/insulin_spatial.png")
+```
+
+## Requirements
+*   scanpy
+*   squidpy
+*   anndata
+*   matplotlib
+
+<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->