hucira 0.0.1

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.

Getting started

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

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 development version:

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

Release notes

See the changelog.

Contact

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

Citation

t.b.a