Co-accessibility network from single-cell ATAC-seq data. Python code with AnnData, based on Cicero algorithm.
☆35May 23, 2026Updated 3 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☆32May 7, 2026Updated 3 months ago
- A novel method for single-cell diagonal integration: scConfluence☆28Nov 3, 2025Updated 10 months ago
- single cell foundation model for Gene network inference and more☆20May 20, 2026Updated 3 months ago
- Camiel's scATAC-seq analysis pipeline☆15Apr 15, 2024Updated 2 years ago
- Learning cell fate landscapes from spatial transcriptomics using Fused Gromov-Wasserstein☆32Oct 21, 2025Updated 10 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Python package for the ICML 2022 paper "Unsupervised Ground Metric Learning Using Wasserstein Singular Vectors".☆10Sep 2, 2024Updated 2 years ago
- A python package for chromVAR☆34May 1, 2023Updated 3 years ago
- Single Cell Pretrained Regulatory network INference from Transcripts☆11Sep 17, 2024Updated last year
- Identifying transcription factor binding sites from neural network contribution scores☆25Aug 26, 2026Updated last week
- ☆15Jun 27, 2025Updated last year
- Unsupervised Deep Disentangled Representation of Single-Cell Omics☆80Updated this week
- Fast and scalable inference for single-cell differential gene expression of multiple patients☆15Jul 3, 2026Updated 2 months ago
- Context specific and dynamic gene regulatory network reconstruction and analysis☆130Aug 3, 2026Updated last month
- Single-cell epigenomics analysis tools☆323Aug 15, 2026Updated 2 weeks ago
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- 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
- Benchmark of GRNs using the GRETA pipeline☆33Jun 9, 2026Updated 2 months ago
- scDoRI (single-cell Deep multi-Omic Regulatory Inference) is a deep learning model to infer enhancer-mediated gene regulatory networks (e…☆35Aug 15, 2026Updated 2 weeks ago
- ☆17Updated this week
- ☆26Jul 15, 2026Updated last month
- Conveniently process a dictionary of anndatas☆23Apr 17, 2026Updated 4 months ago
- Scalable framework for integrating single-cell omics with genetic data using AnnData.☆21Updated this week
- Pareto Task Inference in Python☆23Updated this week
- Supplementary files and notebooks to recreate figures.☆23Aug 4, 2026Updated last month
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- ☆15Mar 2, 2023Updated 3 years ago
- Multiome GRN inference.☆141Apr 10, 2026Updated 4 months ago
- Pipeline to run scE2G☆61Updated this week
- Single-cell multi-omics integration using Optimal Transport☆55Aug 14, 2025Updated last year
- scATAC-seq data analysis tools and papers☆133Jul 1, 2025Updated last year
- Fairness in single-cell data☆21Mar 25, 2026Updated 5 months ago
- scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.☆68Aug 10, 2026Updated 3 weeks ago
- Accurate and fast cell marker gene identification with COSG☆59Aug 24, 2026Updated last week
- AnnData interoperability in R☆195Updated this week
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- R package IReNA☆31Nov 13, 2024Updated last year
- Code & documentation for Multiomics and deep learning dissect regulatory syntax in human development (Liu*, Jessa*, Kim*, Ng*, et al, Nat…☆30Jul 17, 2026Updated last month
- A Python package for unsupervised analysis of spatial (prote)omics data.☆19Jul 23, 2026Updated last month
- A smorgasbord of R functions for performing and teaching population genomic analyses☆19Jan 26, 2026Updated 7 months ago
- muon is a multimodal omics Python framework☆278Updated this week
- Work with trained factor models in Python☆41Oct 22, 2024Updated last year
- SIMBA: SIngle-cell eMBedding Along with features☆20Jan 6, 2026Updated 7 months ago