pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
☆82Jul 9, 2026Updated 2 weeks ago
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…☆261Jan 16, 2026Updated 6 months ago
- pycistarget is a python module to perform motif enrichment analysis in sets of regions with different tools and identify high confidence …☆20Apr 14, 2026Updated 3 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…☆75Jul 3, 2026Updated 3 weeks ago
- Pipeline for Universal Mapping of ATAC-seq☆27Sep 23, 2025Updated 10 months ago
- Genomic Features in Python from BioConductor's AnnotationHub☆23Updated this 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.
- ☆19Dec 15, 2023Updated 2 years ago
- ☆12Sep 7, 2023Updated 2 years ago
- ☆68Apr 22, 2026Updated 3 months ago
- Single-cell epigenomics analysis tools☆323Jul 13, 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☆147Apr 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.☆21Jun 15, 2026Updated last month
- 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.
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆627Jun 26, 2025Updated last year
- Modeling complex perturbations with CellFlow☆151Updated this week
- Aligning gene expression trajectories of single-cell reference and query systems☆89Aug 10, 2025Updated 11 months ago
- A python package for chromVAR☆34May 1, 2023Updated 3 years ago
- ☆15Jun 4, 2023Updated 3 years ago
- ☆75May 27, 2026Updated last month
- ☆27Apr 15, 2025Updated last year
- Create cisTarget databases☆61Jun 18, 2025Updated last year
- scOpen: single-cell open chromatin analysis via NMF modelling☆28Feb 4, 2023Updated 3 years ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- CellRank: dynamics from multi-view single-cell data☆454Jul 16, 2026Updated last week
- This is the alpha version of the CellOracle package☆478Apr 30, 2026Updated 2 months ago
- CAST package☆44Oct 26, 2024Updated last year
- Context specific and dynamic gene regulatory network reconstruction and analysis☆129Updated this week
- Python Toolkit for Transcription Factor Activity Inference and Clustering of scRNA-seq Data☆37Dec 15, 2025Updated 7 months ago
- scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.☆69Apr 1, 2026Updated 3 months ago
- ☆31Sep 22, 2023Updated 2 years ago
- ☆99Updated this week
- ☆20May 12, 2026Updated 2 months ago
- Bare Metal GPUs on DigitalOcean Gradient AI • AdPurpose-built for serious AI teams training foundational models, running large-scale inference, and pushing the boundaries of what's possible.
- Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data☆11Jul 6, 2026Updated 2 weeks ago
- Single-nuclei RNA-seq and ATAC-seq in Alzheimer's disease☆98Jul 1, 2021Updated 5 years 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
- Single-cell perturbation analysis☆338Updated this week
- Episcanpy: Epigenomics Single Cell Analysis in Python☆151Dec 5, 2024Updated last year
- Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromati…☆14Oct 16, 2025Updated 9 months ago