swaruplab/operon - Page 10

cellular-senescence-agent

AI-powered analysis of cellular senescence for aging research, cancer therapy response, and senolytic drug development.

chatehr-clinician-assistant

EHR Chat Assistant

chematagent-drug-discovery

Chemical Lab Agent

chemcrow-drug-discovery

An LLM chemistry agent with expert-designed tools for organic synthesis, drug discovery, and materials design.

chemical-property-lookup

Compute RDKit-driven molecular properties (MW, logP, TPSA, QED, Lipinski) for a SMILES string to support downstream drug discovery tools.

chemist-analyst

Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectroscopy, chromatography, mass spectrometry). Provides insights on chemical processes, material properties,…

chemistry-agent

Autonomous chemical synthesis & analysis

clinical-nlp-extractor

Extracts medical entities (Diseases, Medications, Procedures) from unstructured clinical text using regex and simple rules (or LLM wrappers).

clinical-note-summarization

Structure raw clinical notes into SOAP-format summaries with explicit contradictions, missing data, and ICD-linked assessments using the provided prompt + usage script.

crispr-guide-design

Guide foundry

crispr-offtarget-predictor

Predicts potential off-target sites for a given sgRNA sequence using mismatch analysis.

cryoem-ai-drug-design-agent

AI-powered integration of cryo-EM structural data with generative AI and molecular dynamics for structure-based drug design targeting flexible proteins and membrane complexes.

ctdna-dynamics-mrd-agent

AI-powered circulating tumor DNA dynamics analysis for molecular residual disease detection, treatment response monitoring, and early relapse prediction using liquid biopsy.

data-visualization-biomedical

Publication-quality visualizations for biomedical and genomics data. Use when creating volcano plots, heatmaps, UMAP plots, dot plots, survival curves, forest plots, or multi-panel figures. Includes scanpy, matplotlib, seaborn, plotly workflows with…

deep-visual-proteomics-agent

AI-driven integration of cellular imaging, laser microdissection, and ultra-sensitive mass spectrometry for spatially-resolved single-cell proteomics.

digital-twin-clinical-agent

AI-powered patient digital twin creation for clinical trial simulation, treatment outcome prediction, and personalized medicine using real-world data and multi-omics integration.

drug-interaction-checker

Checks for potential drug-drug interactions (DDIs) between a list of medications.

ehr-fhir-integration

Provides comprehensive tools for working with Electronic Health Records (EHR) using the HL7 FHIR standard.

epigenomics-methylgpt-agent

AI-powered DNA methylation analysis using MethylGPT foundation models for epigenomic profiling, differential methylation detection, and cancer epigenome characterization.

gene-panel-design-agent

AI-powered design of targeted gene panels for clinical and research applications including cancer diagnostics, pharmacogenomics, and rare disease testing.

gwas-lookup

Federated variant lookup across 9 genomic databases — GWAS Catalog, Open Targets, PheWeb (UKB, FinnGen, BBJ), GTEx, eQTL Catalogue, and more.

immune-checkpoint-combination-agent

AI-powered analysis for predicting optimal immune checkpoint inhibitor combinations based on tumor microenvironment, biomarkers, and molecular profiling.

long-read-sequencing-agent

AI-powered analysis of long-read sequencing data (PacBio, ONT) for structural variant detection, isoform discovery, epigenetic modifications, and de novo assembly.

microbiome-cancer-agent

AI-powered analysis of microbiome-cancer interactions including tumor microbiome profiling, immunotherapy response prediction, and microbiome-targeted therapeutic opportunities.

molecular-glue-discovery-agent

AI-powered molecular glue discovery for targeted protein degradation, enabling neo-substrate recruitment and undruggable target degradation through E3 ligase interface modulation.

molecule-evolution-agent

Evolve Molecules

multimodal-medical-imaging

Analyzes medical images (X-ray, MRI, CT) using multimodal LLMs to identify anomalies and generate reports.

nicheformer-spatial-agent

Foundation model-powered spatial transcriptomics analysis leveraging 53M+ spatially resolved cells for cellular architecture modeling and tissue niche discovery.

nk-cell-therapy-agent

AI-powered NK cell therapy design for cancer immunotherapy including CAR-NK engineering, memory-like NK generation, and KIR/HLA matching optimization.

organoid-drug-response-agent

AI-powered analysis of patient-derived organoid (PDO) drug screening for personalized oncology treatment selection and biomarker discovery.

pan-cancer-multiomics-agent

AI-powered pan-cancer analysis integrating genomic, transcriptomic, proteomic, and epigenomic data for cancer subtyping, driver identification, and cross-cancer pattern discovery.

pharmacogenomics-agent

AI-driven pharmacogenomic analysis for precision dosing and adverse event prediction using multi-omics data.

precision-oncology-agent

Fuse genomic variants, pathology findings, and clinical context to draft evidence-linked therapy options for tumor board review.

protein-structure-prediction

Predicts 3D protein structures from amino acid sequences using ESMFold or AlphaFold3 (mock).

rna-velocity-agent

AI-powered RNA velocity analysis for predicting cellular state transitions, differentiation trajectories, and dynamic gene regulation from single-cell RNA sequencing data.

scrna-qc

Execute the MAD-based single-cell RNA-seq QC workflow (scripts + Python API) to filter low-quality cells and emit reports plus filtered AnnData files.

single-cell-rna-qc

Performs quality control on single-cell RNA-seq data (.h5ad or .h5 files) using scverse best practices with MAD-based filtering and comprehensive visualizations. Use when users request QC analysis, filtering low-quality cells, assessing data quality, or…

spatial-agent

An agent that interprets spatial transcriptomics data to propose mechanistic hypotheses and analyze tissue organization.

spatial-epigenomics-agent

AI-powered spatial epigenomics analysis combining chromatin accessibility, histone modifications, and DNA methylation with spatial coordinates for tissue architecture mapping.

spatial-transcriptomics-agent

Spatial analyst