A Python alternative to `clustree` for assessing single-cell RNA-sequencing clusters.
☆19Mar 11, 2026Updated 4 months ago
Alternatives and similar repositories for pyclustree
Users that are interested in pyclustree are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆14Feb 24, 2020Updated 6 years ago
- Read and Write RDS files, in Python☆28Aug 3, 2026Updated last week
- Feature-rich Python implementation of the tximport package for gene count estimation.☆45Jul 10, 2026Updated last month
- Python package to generate high dimensional Flow Cytometry datasets using imputation by XGBoost regression☆13Sep 30, 2024Updated last year
- Wrapper and helper functions to use bulk RNA-seq differential expression methods with single-cell data☆24Feb 4, 2024Updated 2 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.
- A wrapper around the sleepwalk package that allows for interactive knn visualizations of an embedding.☆23May 8, 2024Updated 2 years ago
- A Python package for unsupervised analysis of spatial (prote)omics data.☆19Jul 23, 2026Updated 2 weeks ago
- Gene set scoring for single-cell data☆203Apr 29, 2026Updated 3 months ago
- AI-Driven Code Generation, Explanation and Execution for Data Analysis☆23Sep 11, 2024Updated last year
- Legend made easy for matplotlib☆36Aug 3, 2026Updated last week
- The R package scCODE, a platform for data-specific DE gene detection for scRNA-seq data☆15Nov 9, 2023Updated 2 years ago
- BANKSY: Spatial Clustering Algorithm that Unifies Cell-Typing and Tissue Domain Segmentation. Python package for spatial transcriptomics …☆87Jul 4, 2026Updated last month
- ☆13Aug 9, 2022Updated 4 years ago
- ☆59Nov 1, 2024Updated last year
- 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.
- Perform differential expression analysis on cohort-scale single cell datasets using linear mixed models☆23May 22, 2026Updated 2 months ago
- Quantify and interpret divers of variation in multilevel gene expression experiments☆16Jul 14, 2026Updated 3 weeks ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆80Updated this week
- A deep model infers gene regulation networks from scRNA-seq data.☆12Jul 26, 2026Updated 2 weeks ago
- A Safe Space to Experience Pull Requests☆14Dec 14, 2025Updated 7 months ago
- Coarse-graining of large single-cell RNA-seq data into metacells☆105Apr 16, 2026Updated 3 months ago
- A modular tool for proportion analysis in single-cell sequencing data☆28Feb 26, 2026Updated 5 months ago
- Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT)☆26Updated this week
- Single-cell perturbation analysis☆338Updated this week
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- STAgent is a multimodal LLM-based AI agent that enables deep research about spatial transcriptomics data☆61May 22, 2026Updated 2 months ago
- Registry for scverse ecosystem packages☆38Updated this week
- ☆38Jan 22, 2026Updated 6 months ago
- A tool for semi-automatic cell type classification☆500May 22, 2026Updated 2 months ago
- Phylogenetic analyses code☆10Feb 12, 2020Updated 6 years ago
- R package to do the Ligand Receptor Analysis Visualization☆50Jun 23, 2026Updated last month
- Automated cell filtering for single-cell RNA sequencing data☆26Nov 14, 2023Updated 2 years ago
- Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-…☆57Jun 2, 2026Updated 2 months ago
- Information-based dimensionality reduction☆30Dec 14, 2024Updated last year
- 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.
- A python port of the R package SCTransform:☆21Jul 10, 2021Updated 5 years ago
- Repository for Nicheformer: a foundation model for single-cell and spatial omics☆170Nov 23, 2025Updated 8 months ago
- Calculate cluster similarity between clusters from different single cell datasets/batches/samples.☆26Feb 2, 2026Updated 6 months ago
- Bioinformatics Algorithms☆16Dec 17, 2013Updated 12 years ago
- Multi-resolution Variational Inference☆23Jul 13, 2026Updated 3 weeks ago
- ☆17Sep 16, 2023Updated 2 years ago
- See https://github.com/LTLA/SingleRBook for the latest version of this content.☆14Jun 21, 2022Updated 4 years ago