3. Data, Science & AI

Provides access to ClinPGx pharmacogenomics database for querying gene-drug interactions, CPIC guidelines, and allele functions to support precision medicine decisions.

Provides automated metrics, human feedback, and benchmarking for evaluating LLM application performance and quality.

Extracts flow cytometry data from FCS files, converting events and metadata into structured NumPy arrays and DataFrames for analysis.

Efficiently searches and retrieves life sciences preprints from bioRxiv with keyword, author, date, and category filters for literature reviews.

Comprehensive toolkit for developing, testing, and deploying machine learning models using clinical data, EHR, and healthcare datasets like MIMIC.

Queries PubChem chemical database for compound properties, similarity, and bioactivity using PUG-REST or PubChemPy APIs.

Queries ChEMBL database for bioactive molecules, drug discovery data, and supports SAR studies in medicinal chemistry.

Enables genomics pipeline development and execution on DNAnexus, including data management, workflow runs, and dxpy SDK integration for FASTQ/BAM/VCF processing.

DeepTools is a genomic analysis toolkit for converting BAM to bigWig, performing QC, and generating visualizations for ChIP-seq, RNA-seq, and ATAC-seq data.

Provides AI-ready drug discovery datasets including ADME, toxicity, DTI benchmarks, scaffold splits, and molecular oracles for therapeutic ML models.

Provides access to and analysis of comprehensive drug data from DrugBank, including properties, interactions, targets, and pharmacology for research and discovery.

Provides tools for sequence analysis, phylogenetic trees, microbiome diversity metrics, and statistical tests like UniFrac and PERMANOVA.

Python toolkit for molecular biology data processing, handling sequence manipulation, file parsing (FASTA, GenBank), and BLAST workflows.

Computational materials science toolkit for crystal structure analysis, phase diagrams, band structure, and Materials Project integration.

Provides access to NCBI GEO database for searching, downloading, and retrieving gene expression and genomics datasets including microarray and RNA-seq data.

AI-powered toolkit for analyzing whole-slide images and multiparametric pathology data using ML models, supporting 160+ slide formats and pathology workflows.

Efficient storage and parallel I/O for large N-D arrays in cloud storage (S3/GCS), compatible with NumPy, Dask, and Xarray for scientific computing pipelines.

scvi-tools for single-cell omics data analysis: probabilistic modeling, batch correction, and multimodal integration for scRNA-seq, scATAC-seq, and spatial transcriptomics.

Comprehensive toolkit for protein language models (ESM3, ESM C) enabling sequence, structure, and function prediction, design, and engineering via local or cloud inference.

Processes mass spectrometry data (mzML/MGF/MSP) for metabolomics, enabling spectral similarity calculations and compound identification.

Provides programmatic access to Data Commons for querying global statistical data including demographics, economics, health, and environmental metrics.

PyTorch-based toolkit for graph neural networks in drug discovery, enabling molecular property prediction, protein modeling, and molecular generation.

Phylogenetic tree toolkit for manipulating trees (Newick/NHX), detecting evolutionary events, and visualizing phylogenomic data.

Provides Python-based tools for reading, writing, and analyzing genomic data formats including SAM/BAM, VCF, and FASTQ in next-generation sequencing workflows.