Data & Analytics

Unified Python access to 40+ bioinformatics web services; use when you need to query multiple databases (e.g., UniProt/KEGG/ChEMBL/Reactome) with one consistent API in a single workflow, especially for cross-database analysis and identifier mapping.

A comprehensive toolbox for computational molecular biology; use it when you need programmatic sequence/structure parsing, batch bioinformatics pipelines, or automated NCBI/BLAST workflows.

Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural comparison/superposition.

Use Biopython to read/write/convert biological sequence files (FASTA/GenBank/FASTQ, etc.) and perform basic sequence operations; use when you need reliable sequence I/O, lightweight sequence manipulation, or scalable processing of large sequence datasets.

Use Bio.Phylo to read/write phylogenetic trees and perform visualization and statistics; use when tree parsing/conversion, pruning/rerooting, distance calculation, or plotting is required.

Sequence alignment and alignment file processing with Biopython (Bio.Align/Bio.AlignIO), triggered when you need global/local pairwise alignment, MSA read/write/format conversion, or alignment statistics/filtering.

Advanced Biopython modules for motifs, population genetics, sequence utilities, restriction analysis, clustering, and GenomeDiagram visualization; use when you need extended bioinformatics analysis beyond basic sequence I/O and alignment.

Detect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger filtering for variant directionality. Use when validating MR results, detecting pleiotropic instrum...

Decompose genetic effects into direct and indirect paths through mediating variables using the mediation R package. Tests whether gene expression, methylation, or other molecular phenotypes mediate the effect of genetic variants on disease. Use when testing whether a molecular...

Extracts clinical trial baseline data (study, region, participants, etc.) from article text or PMID. Checks PubMed for metadata; always falls back to LLM extraction for full details.

Data structure for annotated matrices in single-cell analysis; use when reading/writing .h5ad (or zarr) and exchanging data with the scverse ecosystem.

Analyze data with `adme-property-predictor` using a reproducible workflow, explicit validation, and structured outputs for review-ready interpretation.

PyTorch-native Graph Neural Network framework for molecules and proteins. Suitable for building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, and retrosynthesis. If you need pretrained models and diverse feature extractors, use deepchem; if you need benchmark datasets, use pytdc.

Clinical Research Bias Assessment - Case-Control Study (NOS) v2.3.0. Use when you need to assess the bias of a case-control study using the Newcastle-Ottawa Scale (NOS) criteria, or when evaluating the quality of a medical paper.

Generate photorealistic rendering scripts for PyMOL and UCSF ChimeraX.

Generates detailed text descriptions of medical images and charts for.

Generate USMLE Step 1/2 style clinical cases with patient history, physical.

Use when converting medical text between academic and patient-friendly tones, translating medical jargon for patients, adapting research papers for public audiences, or rewriting clinical notes for patient handouts. Maintains medical accuracy while adjusting readability level.

Orchestrates a systematic review and meta-analysis workflow following PRISMA 2020 guidelines, from protocol development through multi-database search, screening, data extraction, and evidence synthesis. Use when conducting evidence-based reviews, meta-analyses, or scoping revi...

Rewrite drafts according to target writing style or target journal format. Triggers when user says "rewrite in XX style", "match this tone", "format for XX journal", "rewrite following this format". Input can be .docx / .md / .txt or conversation text.

Use study limitations drafter for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.

Use semantic consistency auditor for academic writing workflows that need structured execution, explicit assumptions, and clear output boundaries.

Advanced sample size and power calculations for complex study designs including survival analysis, clustered designs, and multiple comparisons.

Polish reviewer-response letters by softening defensive language, preserving factual meaning, and keeping responses professional, concise, and publication-appropriate.