Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.
☆34Mar 4, 2026Updated 3 weeks 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☆30Jan 14, 2026Updated 2 months ago
- A novel method for single-cell diagonal integration: scConfluence☆26Nov 3, 2025Updated 4 months ago
- single cell foundation model for Gene network inference and more☆20Nov 24, 2025Updated 4 months ago
- Camiel's scATAC-seq analysis pipeline☆13Apr 15, 2024Updated last year
- Learning cell fate landscapes from spatial transcriptomics using Fused Gromov-Wasserstein☆25Oct 21, 2025Updated 5 months ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- A python package for chromVAR☆33May 1, 2023Updated 2 years ago
- Single Cell Pretrained Regulatory network INference from Transcripts☆11Sep 17, 2024Updated last year
- Python package for the ICML 2022 paper "Unsupervised Ground Metric Learning Using Wasserstein Singular Vectors".☆10Sep 2, 2024Updated last year
- ☆15Jun 27, 2025Updated 8 months ago
- Single-cell epigenomics analysis tools☆311Mar 13, 2026Updated 2 weeks ago
- Unsupervised Deep Disentangled Representation of Single-Cell Omics☆61Updated this week
- Pipeline to run scE2G☆37Feb 4, 2026Updated last month
- This Python package will allow you to replicate the experiments from our research on applying Optimal Transport as a similarity metric in…☆43Feb 3, 2023Updated 3 years ago
- Context specific and dynamic gene regulatory network reconstruction and analysis☆128Mar 9, 2026Updated 2 weeks ago
- DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- ☆15Nov 24, 2025Updated 4 months ago
- Supplementary files and notebooks to recreate figures.☆21Aug 12, 2025Updated 7 months ago
- ☆16Mar 2, 2023Updated 3 years ago
- Multiome GRN inference.☆133Apr 19, 2024Updated last year
- scATAC-seq data analysis tools and papers☆129Jul 1, 2025Updated 8 months ago
- Single-cell multi-omics integration using Optimal Transport☆51Aug 14, 2025Updated 7 months ago
- ☆27Jul 2, 2024Updated last year
- scNODE: Generative Model for Temporal Single Cell Transcriptomic Data Prediction☆30Oct 11, 2024Updated last year
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆78Mar 12, 2026Updated 2 weeks ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- scCellFie infers metabolic activities from single-cell and spatial transcriptomics and offers a variety of downstream analyses.☆53Jan 24, 2026Updated 2 months ago
- R package IReNA☆29Nov 13, 2024Updated last year
- A smorgasbord of R functions for performing and teaching population genomic analyses☆19Jan 26, 2026Updated 2 months ago
- ☆28Mar 20, 2026Updated last week
- muon is a multimodal omics Python framework☆265Mar 16, 2026Updated last week
- An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)☆38Aug 22, 2024Updated last year
- Translates an AnnData object with mouse gene symbols into one with human gene symbols by mapping orthologs from biomart.☆29Jun 10, 2025Updated 9 months ago
- ☆32Oct 4, 2024Updated last year
- SIMBA: SIngle-cell eMBedding Along with features☆20Jan 6, 2026Updated 2 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Basics of the OSCA book☆14Sep 29, 2025Updated 5 months ago
- Elucidating the Utility of Genomic Elements with Neural Nets☆69Dec 2, 2024Updated last year
- Work with trained factor models in Python☆39Oct 22, 2024Updated last year
- AnnData interoperability in R☆164Mar 18, 2026Updated last week
- Code for the paper: "Abide by the Law and Follow the Flow: Conservation Laws for Gradient Flows".☆12Feb 24, 2024Updated 2 years ago
- Episcanpy: Epigenomics Single Cell Analysis in Python☆151Dec 5, 2024Updated last year
- ☆12Nov 13, 2024Updated last year