CIRCE is a Python package based on #AnnData and fully compatible with the #scverse environment.

You can extract DNA region modules & visualize CIRCE's interactions over gene locations.

CIRCE also facilitates #CellOracle or #HuMMuS usage, making it unnecessary to run Cicero (code in R) first.

4/5

We explore the impact of preprocessing on DNA interactions inference. 👩‍🔬

We evaluated scATAC-seq preprocessings using promoter capture Hi-C data. 🧬

TLDR: Best performance came from single-cell inputs directly and from CIRCE metacells! 📊
In contrast, count normalization had a negative impact.

3/5

We compared CIRCE & Cicero on 2 datasets, demonstrating near identical results from the same input.

Both use pseudo-cells to reduce sparsity. CIRCE proposes a new strategy, whose output is closer to the single-cell profiles. 🛠️

On average, CIRCE uses 5x less memory and runs 150x faster ! 📈

2/5

I'm presenting #CIRCE, a Python package to infer co-accessible DNA region networks 🧬

Based on #Cicero 's algorithm (Pliner et al.), it runs ~150x faster, processing an atlas of 700k cells in less than 40 min! ⛷️

Short paper: doi.org/10.1101/2025...
Code: github.com/cantinilab/CIRCE

1/5 ⬇️