Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.
☆37May 23, 2026Updated 5 months ago
Alternatives and similar repositories for Circe
Users that are interested in Circe are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Molecular interactions inference from single-cell multi-omics data☆33May 7, 2026Updated 5 months ago
- A novel method for single-cell diagonal integration: scConfluence☆30Nov 3, 2025Updated last year
- A python package for chromVAR☆36May 1, 2023Updated 3 years ago
- scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (e…☆39Aug 15, 2026Updated 2 months ago
- Analysis of epigenetic data in Python☆15Oct 28, 2026Updated last week
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- single cell foundation model for Gene network inference and more☆20May 20, 2026Updated 5 months ago
- ☆17Updated this week
- Camiel's scATAC-seq analysis pipeline☆15Apr 15, 2024Updated 2 years ago
- ☆15Jun 27, 2025Updated last year
- Learning cell fate landscapes from spatial transcriptomics using Fused Gromov-Wasserstein☆32Oct 21, 2025Updated last year
- Pareto Task Inference in Python☆23Updated this week
- ☆16Apr 8, 2026Updated 6 months ago
- Analysis framework for morphological profiling data☆15Updated this week
- Python package for the ICML 2022 paper "Unsupervised Ground Metric Learning Using Wasserstein Singular Vectors".☆10Sep 2, 2024Updated 2 years ago
- Deploy open-source AI quickly and easily - Special Bonus Offer • AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- Single-cell epigenomics analysis tools☆329Sep 12, 2026Updated last month
- Single Cell Pretrained Regulatory network INference from Transcripts☆11Sep 17, 2024Updated 2 years ago
- Unsupervised Deep Disentangled Representation of Single-Cell Omics☆83Oct 26, 2026Updated last week
- Identifying transcription factor binding sites from neural network contribution scores☆28Aug 26, 2026Updated 2 months ago
- Benchmark of GRNs using the GRETA pipeline☆33Jun 9, 2026Updated 4 months ago
- A command-line tool to capture hierarchical relationships at scale☆20Updated this week
- scATAC-seq data analysis tools and papers☆133Jul 1, 2025Updated last year
- Simple scVI implementation☆13Oct 19, 2026Updated 2 weeks ago
- Pipeline to run scE2G☆69Oct 27, 2026Updated last week
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Context specific and dynamic gene regulatory network reconstruction and analysis☆135Aug 3, 2026Updated 3 months ago
- Scalable framework for integrating single-cell omics with genetic data using AnnData.☆25Updated this week
- An AnnData-based framework for integrated proteomics analysis☆30Updated this week
- A composite regression neural network for latent timing prediction of single-cell RNA-seq data☆10Jan 21, 2025Updated last year
- Fast and scalable inference for single-cell differential gene expression of multiple patients☆15Jul 3, 2026Updated 4 months ago
- AnnNet (Annotated Network) is a unified, high-expressivity graph platform designed to bring the convenience of AnnData-style annotated co…☆25Oct 11, 2026Updated 3 weeks ago
- ☆11Jan 22, 2026Updated 9 months ago
- ☆17Oct 22, 2026Updated 2 weeks ago
- Repository for edgePython which is a Python implementation of the Bioconductor edgeR package for differential analysis of genomics count …☆104Oct 25, 2026Updated last week
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Awesome GRN enhanced AnnData toolkit☆13Feb 19, 2026Updated 8 months ago
- Single-cell multi-omics integration using Optimal Transport☆56Aug 14, 2025Updated last year
- Universal Single-Cell Genomics Preprocessing package☆53Updated this week
- A Python package for unsupervised analysis of spatial (prote)omics data.☆19Oct 26, 2026Updated last week
- ☆12Jan 31, 2023Updated 3 years ago
- ☆16Updated this week
- ☆13Aug 11, 2025Updated last year