pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
☆84Sep 15, 2026Updated last week
Alternatives and similar repositories for pycisTopic
Users that are interested in pycisTopic are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆264Jan 16, 2026Updated 8 months ago
- pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence …☆21Apr 14, 2026Updated 5 months ago
- CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for desi…☆81Sep 15, 2026Updated last week
- Pipeline for Universal Mapping of ATAC-seq☆27Sep 23, 2025Updated last year
- Genomic Features in Python from BioConductor's AnnotationHub☆22Sep 14, 2026Updated last week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- ☆19Dec 15, 2023Updated 2 years ago
- ☆12Sep 7, 2023Updated 3 years ago
- ☆69Apr 22, 2026Updated 5 months ago
- Single-cell epigenomics analysis tools☆323Sep 12, 2026Updated last week
- Parse ArchR arrow files to anndata h5ad☆16Dec 14, 2023Updated 2 years ago
- cisTopic: Probabilistic modelling of cis-regulatory topics from single cell epigenomics data☆148Apr 5, 2024Updated 2 years ago
- k-NN-based mapping of cells across representations to transfer labels, embeddings, and expression values.☆16Updated this week
- Code for scKINETICS (ISMB 2023)☆22Oct 23, 2023Updated 2 years ago
- Supplementary files and notebooks to recreate figures.☆23Aug 4, 2026Updated last month
- 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.
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆638Jun 26, 2025Updated last year
- Modeling complex perturbations with CellFlow☆159Updated this week
- Aligning gene expression trajectories of single-cell reference and query systems☆93Jul 28, 2026Updated last month
- A python package for chromVAR☆35May 1, 2023Updated 3 years ago
- ☆15Jun 4, 2023Updated 3 years ago
- ☆79May 27, 2026Updated 3 months ago
- ☆27Apr 15, 2025Updated last year
- Create cisTarget databases☆63Jun 18, 2025Updated last year
- scOpen: single-cell open chromatin analysis via NMF modelling☆28Feb 4, 2023Updated 3 years 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.
- Single-nuclei RNA-seq and ATAC-seq in Alzheimer's disease☆99Jul 1, 2021Updated 5 years ago
- CellRank: dynamics from multi-view single-cell data☆456Sep 16, 2026Updated last week
- This is the alpha version of the CellOracle package☆500Apr 30, 2026Updated 4 months ago
- CAST package☆43Oct 26, 2024Updated last year
- Context specific and dynamic gene regulatory network reconstruction and analysis☆132Aug 3, 2026Updated last month
- Python Toolkit for Transcription Factor Activity Inference and Clustering of scRNA-seq Data☆36Dec 15, 2025Updated 9 months ago
- scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.☆68Aug 10, 2026Updated last month
- ☆31Sep 22, 2023Updated 3 years ago
- ☆102Updated this week
- End-to-end encrypted email - Proton Mail • AdSpecial offer: 40% Off Yearly / 80% Off First Month. All Proton services are open source and independently audited for security.
- Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data☆11Jul 6, 2026Updated 2 months ago
- ☆20Aug 25, 2026Updated 3 weeks ago
- JSON-based FON (Feature Object Notation) format and tools to simplify genomic annotations usage☆13Jun 11, 2025Updated last year
- ☆35Oct 4, 2024Updated last year
- Episcanpy: Epigenomics Single Cell Analysis in Python☆153Dec 5, 2024Updated last year
- Single-cell perturbation analysis☆346Updated this week
- Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromati…☆16Oct 16, 2025Updated 11 months ago