expression-atlas 0.1.0

Python client for searching and downloading gene expression datasets from EMBL-EBI Expression Atlas

Expression Atlas Python Client

Python client for searching and downloading gene expression datasets from EMBL-EBI Expression Atlas, mirroring the R Bioconductor package.

Features

• Search for Expression Atlas experiments by properties and species
• Download RNA-seq and microarray experiment data
• R-compatible data structures: SummarizedExperiment (RNA-seq) and ExpressionSet (microarray) wrapped in SimpleList
• Sync API with full type hints

Installation

pip install expression-atlas

For development:

pip install -e ".[dev]"

Quick Start

from expression_atlas import ExpressionAtlasClient

client = ExpressionAtlasClient()

# Search experiments (DataFrame with Accession/Species/Type/Title)
results = client.search_experiments(properties=["cancer"], species="homo sapiens")

# Download a single experiment (SimpleList)
exp = client.get_experiment("E-MTAB-1624")

# RNA-seq example
rnaseq = exp["rnaseq"]  # SummarizedExperiment
counts = rnaseq.assays["counts"]  # numpy array genes × samples
sample_annotations = rnaseq.colData

# Microarray example
eset = exp["A-AFFY-126"]  # ExpressionSet
exprs = eset.exprs  # probes × samples
pheno = eset.phenoData

# Multiple experiments
exps = client.get_experiments(["E-MTAB-1624", "E-MTAB-1625"])

Data Structures

RNA-seq Data

RNA-seq experiments are returned as SummarizedExperiment objects containing:

• assays["counts"]: genes × samples matrix (orientation matches R package)
• colData: sample annotations
• rowData: gene annotations

Microarray Data

Microarray experiments are returned as ExpressionSet objects containing:

• exprs: probes × samples matrix (orientation matches R package)
• phenoData: sample annotations
• featureData: probe annotations

API Reference

ExpressionAtlasClient

search_experiments(properties, species=None)

Search for experiments matching given properties.

Parameters:

• properties: List of search terms (e.g., ["cancer", "breast"])
• species: Optional species filter (e.g., "homo sapiens")

Returns: pandas.DataFrame with columns: Accession, Species, Type, Title

get_experiment(accession)

Download a single experiment.

Parameters:

• accession: ArrayExpress/BioStudies accession (e.g., "E-MTAB-1624")

Returns: ExperimentSummary object

get_experiments(accessions)

Download multiple experiments.

Parameters:

• accessions: List of accessions

Returns: Dictionary mapping accessions to ExperimentSummary objects

License

GPL-3.0-or-later

Links

• Expression Atlas
• BioStudies
• Contact Support