Documentation Index
Fetch the complete documentation index at: https://docs.mithrl.com/llms.txt
Use this file to discover all available pages before exploring further.
🗂️ Feature Table
This table provides an at-a-glance view of what Mithrl supports today, what’s in beta, and what’s on the roadmap. Features span the full discovery and development pipeline: from RNA-seq through multi-omics, and into downstream clinical programs.
We iterate fast. If there’s a feature your team needs sooner, reach out to your Customer Success Manager.
✅ Legend
| Symbol | Status |
|---|
| ✅ | Fully supported |
| 🧪 | Beta (available on request) |
| 🔜 | On roadmap (not yet released) |
🔎 Feature Overview
| Feature | Status | Data Types | Description |
|---|
| Exploratory Data Analysis | ✅ | Bulk, scRNA-seq | Sample QC, normalization, outlier detection |
| Differential Expression | ✅ | Bulk, scRNA-seq | Identify genes altered by treatment |
| Functional Enrichment | ✅ | Bulk, scRNA-seq | KEGG/Reactome/GO pathway analysis of DEGs |
| Target Discovery | ✅ | Bulk, scRNA-seq, PPI networks, Curated knowledge bases | Rank and prioritize genes using networks, enrichment, and literature |
| Protein-Protein Interaction | ✅ | Bulk, scRNA-seq | Visualize gene interaction networks and identify hubs or regulators |
| Clustering | ✅ | Bulk, scRNA-seq | Group similar samples or cells by expression profile |
| Dimensionality Reduction | ✅ | Bulk, scRNA-seq | Visualize structure using PCA, UMAP, or t-SNE |
| Cell Type Identification | ✅ | scRNA-seq | Match cell clusters to reference annotations from public atlases |
| Molecular Subtyping | 🧪 | Bulk | Classify tumor/cell type based on canonical subtype models (e.g., PAM50) |
| Discovery Engine | 🧪 | All | Auto-surface known associations, drug links, and co-expression via LLMs |
| WGS/WES Analysis | 🔜 | Genomic | Detect mutations and structural variants; link to transcriptomic impact |
| DNA Methylation (Bulk + sc) | 🔜 | Epigenomic | Identify differentially methylated regions and correlate with gene activity |
| Proteomics Integration | 🔜 | Proteomic | Connect transcript expression to protein-level data and changes |
| Metabolomics Integration | 🔜 | Metabolomic | Map transcriptomic shifts to metabolic pathways and readouts |
| Multi-Omics Cohort Analysis | 🔜 | Multi-omics | Merge multiple omics (e.g., RNA, methylation, protein) into unified analysis |
| Lead Optimization AI | 🔜 | Downstream | Suggest lead molecules based on gene signature, pathway response, and SAR overlays |
| High-Throughput Screening AI | 🔜 | Downstream | Interpret large HTS datasets using AI-guided dimensionality reduction, target filtering, and phenotypic enrichment |
| IND Support AI | 🔜 | Preclinical | Identify toxicogenomic signatures, validate biomarkers across species, and generate IND-ready transcriptomic justifications |
| Clinical Trial Analysis AI | 🔜 | Clinical | Stratify trial arms, match molecular subtypes to response groups, identify responder biomarkers, and generate trial decision support summaries |
🔄 Feature Availability by Workflow Stage
| Feature | Status | Notes |
|---|
| Exploratory Data Analysis | ✅ | Includes normalization, QC plots, sample filtering |
| Cell Type Identification | 🧪 | Uses marker gene scoring and optional references |
| Dimensionality Reduction | ✅ | Supports PCA, UMAP, t-SNE, PACMAP |
| Feature | Status | Notes |
|---|
| Differential Expression | ✅ | DESeq2 (bulk), Wilcoxon (scRNA) |
| Clustering | ✅ | Leiden/Louvain supported |
| Molecular Subtyping | 🧪 | PAM50, with more to come |
| Feature | Status | Notes |
|---|
| Functional Enrichment | ✅ | KEGG-based analysis with overlays |
| Protein-Protein Interaction | ✅ | Includes hub identification |
| Target Discovery | ✅ | Integrates expression, networks, and literature |
| Discovery Engine | 🧪 | RAG-powered literature summarization |
| Feature | Status | Notes |
|---|
| Clinical Validation Tools | 🔜 | Scoring gene safety, selectivity, and expression specificity |
| Combination Therapy Modeling | 🔜 | Detect synergy from co-perturbed pathways |
| Proprietary Knowledge Graph | 🔜 | Unifies internal + public annotations and relationships |
📌 Notes
- Beta features may change rapidly and could return incomplete results under certain conditions.
- Roadmap features are under development and subject to change based on customer input.
- You can request access to beta tools via your Customer Success channel.
