> For the complete documentation index, see [llms.txt](https://docs.mithrl.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.mithrl.com/platform/supported-features.md).

# Supported Features

The following is a list of supported features

We iterate fast. If there's a feature your team needs sooner, reach out to your Customer Success Manager or contact us at <support@mithrl.com>

## Feature Overview

<table><thead><tr><th width="187">Feature</th><th width="154.6015625">Status</th><th width="201.0078125">Data Types</th><th>Description</th><th data-hidden data-type="image">Cover image</th></tr></thead><tbody><tr><td><strong>Exploratory Data Analysis (EDA)</strong></td><td>✅ Supported</td><td>Bulk, scRNA-seq, Proteomics, DRUG-seq, Code-Omics</td><td>Supporting QC, normalization, ample filtering, and outlier detection.</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>Differential Expression Analysis (DEA)</strong></td><td>✅ Supported</td><td>Bulk, scRNA-seq, Proteomics, DRUG-seq, Code-Omics</td><td>Supports Bulk RNA-seq (DESeq2, Limma, pseudobulk counts. scRNA-seq (cell type specific Wilcoxon rank-sum. Proteomics, DrugSeq, CodeOmics</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>Functional Enrichment Analysis (FEA)</strong></td><td>✅ Supported</td><td>Bulk, scRNA-seq, Proteomics, DRUG-seq, Code-Omics</td><td>Performs Gene Set Enrichment Analysis (GSEA) and Over-Representation Analysis (ORA) to identify enriched biological processes, molecular functions, and cellular components from your expression or abundance data. Outputs enrichment bar charts, pathway and gene set overlays and gene-set relationship tables. KEGG-based analysis with overlays.</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>Target Discovery</strong></td><td>✅ Supported</td><td>Bulk, scRNA-seq, Proteomics, DRUG-seq, Code-Omics</td><td>Supporting raw fastq or expression matrix files (h5ad, csv, etc) as input to infer PPI networks and predicted targets. Integrates expression networks and literature.</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>Protein-Protein Interaction</strong></td><td>✅ Supported</td><td>Bulk, scRNA-seq, Proteomics, DRUG-seq, Code-Omics</td><td>Visualize gene interaction networks and identify hubs or regulators based on expression data.</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>Clustering Analysis</strong></td><td>✅ Supported</td><td>Bulk, scRNA-seq, Proteomics, DRUG-seq, Code-Omics</td><td>Group similar samples or cells by expression profile. Leiden/Louvain supported</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>Dimensionality Reduction</strong></td><td>✅ Supported</td><td>Bulk, scRNA-seq, Proteomics, DRUG-seq, Code-Omics</td><td>Visualize structure using PCA, UMAP, t-SNE, or PACMAP.</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>Cell Type Identification</strong></td><td>✅ Supported</td><td>scRNA-seq</td><td>Match cell clusters to reference annotations from public atlases. uses marker gene scoring and optional references.</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>Discovery Engine</strong></td><td>✅ Supported</td><td>All</td><td>Leveraging the power of Mithrl's Lattice Knowledge Graph to auto-surface known &#x26; predicted associations, drug links, and co-expression via the knowledge inference engine.</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>WGS/WES Analysis</strong></td><td>🔜 Coming Soon</td><td>Genomic</td><td>Detect mutations and structural variants; link to transcriptomic impact</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>DNA Methylation (Bulk + sc)</strong></td><td>🔜 Coming Soon</td><td>Epigenomic</td><td>Identify differentially methylated regions and correlate with gene activity</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>Proteomics Integration</strong></td><td>🔜 Coming Soon</td><td>Proteomic</td><td>Connect transcript expression to protein-level data and changes</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>Metabolomics Integration</strong></td><td>🔜 Coming Soon</td><td>Metabolomic</td><td>Map transcriptomic shifts to metabolic pathways and readouts</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>Multi-Omics Cohort Analysis</strong></td><td>🔜 Coming Soon</td><td>Multi-omics</td><td>Analyze across multiple omics (e.g., RNA, DNA, protein) into unified analysis</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>Lead Optimization AI</strong></td><td>🔜 Coming Soon</td><td>Downstream</td><td>Suggest lead molecules based on gene signature, pathway response, and SAR overlays</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>High-Throughput Screening AI</strong></td><td>🔜 Coming Soon</td><td>Downstream</td><td>Interpret large HTS datasets using AI-guided dimensionality reduction, target filtering, and phenotypic enrichment</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>IND Support AI</strong></td><td>🔜 Coming Soon</td><td>Preclinical</td><td>Identify toxicogenomic signatures, validate biomarkers across species, and generate IND-ready transcriptomic justifications</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr><tr><td><strong>Clinical Trial Analysis AI</strong></td><td>🔜 Coming Soon</td><td>Clinical</td><td>Stratify trial arms, match molecular subtypes to response groups, identify responder biomarkers, and generate trial decision support summaries</td><td><a href="/files/LXkPLpqmxwiBEeAnmuKJ">/files/LXkPLpqmxwiBEeAnmuKJ</a></td></tr></tbody></table>

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Still have questions? We have answers. Contact us at <support@mithrl.com>
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