Pythiomics API

Programmatic access to a curated multi-omics database of 10,000+ datasets for Jupyter Notebook and RStudio environments.

Overview

The Pythiomics API is a software package developed by Pythia BioSciences that provides programmatic access to Pythiomics, a well-curated and standardized multi-omics database containing more than 10,000 datasets. It is purpose-built for computational biologists and bioinformaticians who need reliable, harmonized omics data integrated directly into their existing analysis environments.

By connecting natively to tools such as Jupyter Notebook and RStudio, the Pythiomics API enables researchers to retrieve, query, and compute against a trusted data source without leaving their preferred workflows. Results can be returned in multiple formats, including text-based matrix files, XML, and JSON, making it straightforward to incorporate into custom pipelines or large-scale analyses.

Supported Data Types

Bulk RNA — currently available
Single-cell RNA — currently available
Proteomics — currently available
Visium Spatial — currently available
CosMx — currently available
Visium HD & Xenium — coming soon
Metabolomics — coming soon
ATAC-Seq & CITE-Seq — coming soon
CHIP-Seq — coming soon
Mutation & GWAS — coming soon

Key Capabilities

Programmatic access to 10,000+ multi-omics datasets from a single, standardized source
Direct integration with native bioinformatics environments including Jupyter Notebook and RStudio
Flexible output formats: text-based matrix files, XML, and JSON
Data that is meticulously curated, harmonized, and quality-controlled for research confidence
Supports custom workflow development and large-scale computational analyses

Who It Is For

Computational biologists building bespoke analysis pipelines
Bioinformaticians running large-scale omics studies
Research teams seeking a reliable, publish-ready data source for multi-omics investigations

The Pythiomics API is available via a trial request directly from Pythia BioSciences, allowing teams to evaluate programmatic access to the Pythiomics database before committing to full deployment within their computational infrastructure.