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tme-immune-profiling-agent

Maintainer FreedomIntelligence · Last updated April 1, 2026

Tumor microenvironment immune profiling: cell type deconvolution and spatial mapping.

OpenClawNanoClawAnalysisReproductiontme-immune-profiling-agent🧠 bioos extended suiteimmunology & cell therapytumor

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/tme-immune-profiling-agent

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • The TME Immune Profiling Agent provides comprehensive tumor microenvironment (TME) immune profiling by integrating multiple data modalities including bulk RNA-seq deconvolution, single-cell transcriptomics, spatial transcriptomics, and multiplex immunofluorescence. It enables biomarker discovery for immunotherapy response and TME-based patient stratification.
  • When characterizing immune composition of tumor microenvironment.
  • For predicting immunotherapy response from TME profiles.
  • To identify immune cell states and functional programs.
  • When analyzing spatial organization of immune infiltrates.

Source Doc

Excerpt From SKILL.md

Core Capabilities

  1. Bulk Deconvolution: Estimate immune cell fractions from bulk RNA-seq.

  2. Single-Cell Immune Profiling: Deep characterization of immune populations.

  3. Spatial Immune Architecture: Map immune cell locations and neighborhoods.

  4. Immune Phenotype Classification: Hot/cold/excluded tumor classification.

  5. Functional State Analysis: Exhaustion, activation, memory signatures.

  6. Response Prediction: Multi-modal immunotherapy response models.

Immune Cell Types Profiled

Cell TypeSubtypesKey Markers
T cellsCD8+, CD4+, Treg, Th1/2/17CD3, CD8, CD4, FOXP3
B cellsNaive, memory, plasmaCD19, CD20, CD138
NK cellsCD56bright, CD56dimNKG7, NCAM1
MacrophagesM1, M2, TAMCD68, CD163, CD206
DendriticcDC1, cDC2, pDCCLEC9A, CD1C, BDCA2
MDSCM-MDSC, PMN-MDSCCD33, CD11b, ARG1
CAFmyCAF, iCAF, apCAFFAP, ACTA2, COL1A1

Deconvolution Methods

MethodAlgorithmCell TypesBest For
CIBERSORTxSVR22Gold standard
xCellssGSEA64Comprehensive
EPICConstrained regression8Tumor/stroma
MCP-counterMarker genes10Robust scores
quanTIseqDeconvolution10Pan-cancer
TIMER2.0MultipleVariableIntegrated

Use cases

  • When characteri.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • TCR_Repertoire_Analysis_Agent - T cell specificity
  • TCell_Exhaustion_Analysis_Agent - Exhaustion phenotyping
  • Spatial_Epigenomics_Agent - Spatial analysis
  • Nicheformer_Spatial_Agent - Spatial foundation models

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