hucira 0.1.1

Human Cytokine Dictionary

huCIRA

huCIRA (human Cytokine Immune Response Analysis) provides an easy-to-use interface to analyze cytokine signaling and cytokine-induced immune program enrichment in transcriptomic datasets.

To get started, simply supply a transcriptomic dataset annotated with immune cell types and the experimental conditions of interest. Using our dictionary as a reference, huCIRA allows you to infer differential cytokine activity and immune program activation across conditions and to map cytokine-mediated interactions between immune cells. Under the hood, huCIRA is based on gseapy to run enrichment analyses.

Demo

Please refer to this tutorial for an example of a full pipeline and outputs.

The core analysis is happening here:

import scanpy as sc
import hucira as hc

# 1. Load your data
adata = sc.read_h5ad("your_transcriptome.h5ad")
human_cytokine_dictionary = hc.load_human_cytokine_dict()

# 2. Run cytokine enrichment analysis for B cells between healthy and diseased patients
enrichment_results = hc.run_one_enrichment_test(
    adata = adata,
    df_hcd_all = human_cytokine_dictionary,
    contrasts_combo = ("healthy", "disease"),
    celltype_combo = ("B cell", "B"),
    contrast_column = "condition",
    celltype_column = "cell_type",
    direction = "upregulated",
    threshold_expression = 0.0
)

# 3. Investigate enrichment scores of cytokines in your data
enrichment_results

Installation

You need to have 3.11 <= Python < 3.14 installed on your system. If you don't have Python installed, we recommend installing uv.

There are several alternative options to install hucira:

1. Install the latest release of hucira from PyPI:

pip install hucira

2. Install the latest development version:

pip install git+https://github.com/theislab/huCIRA.git@main

Installation is expected to complete within a few minutes.

Release notes

See the changelog.

Contact

If you found a bug, please use the issue tracker.

Citation

@article {Oesinghaus2025.12.12.693897,
	author = {Oesinghaus, Lukas and Becker, S{\"o}ren and Vornholz, Larsen and Papalexi, Efthymia and Pangallo, Joey and Moinfar, Amir Ali and Liu, Jenni and Fleur, Alyssa La and Shulman, Maiia and Marrujo, Simone and Hariadi, Bryan and Curca, Crina and Suyama, Alexa and Nigos, Maria and Sanderson, Oliver and Nguyen, Hoai and Tran, Vuong K and Sapre, Ajay A. and Kaplan, Olivia and Schroeder, Sarah and Salvino, Alec and Gallareta-Olivares, Guillermo and Koehler, Ryan and Geiss, Gary and Rosenberg, Alexander B. and Roco, Charles M. and Seelig, Georg and Theis, Fabian},
	title = {A single-cell cytokine dictionary of human peripheral blood},
	elocation-id = {2025.12.12.693897},
	year = {2025},
	doi = {10.64898/2025.12.12.693897},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2025/12/15/2025.12.12.693897},
	journal = {bioRxiv}
}