Mapping out the coarse-grained connectivity structures of complex manifolds.
☆242May 23, 2020Updated 6 years ago
Alternatives and similar repositories for paga
Users that are interested in paga are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- RNA Velocity generalized through dynamical modeling☆499Feb 25, 2026Updated 2 months ago
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆334Apr 23, 2024Updated 2 years ago
- ☆362Dec 9, 2021Updated 4 years ago
- A collection of 50+ trajectory inference methods within a common interface 📥📤☆132Dec 21, 2023Updated 2 years ago
- Episcanpy: Epigenomics Single Cell Analysis in Python☆151Dec 5, 2024Updated last year
- 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 for detecting doublets in single-cell RNA sequencing data☆548Mar 21, 2025Updated last year
- Regulatory networks with Direct Information in python☆41Mar 9, 2023Updated 3 years ago
- RNA velocity estimation in Python☆176Oct 7, 2025Updated 7 months ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆650May 12, 2026Updated last week
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated 10 months ago
- Single-cell Hierarchical Poisson Factorization☆74Feb 14, 2026Updated 3 months ago
- Tools and methods for analysis of single cell assay data in R☆263Oct 17, 2025Updated 7 months ago
- NicheNet: predict active ligand-target links between interacting cells☆646Nov 12, 2025Updated 6 months ago
- Single-cell analysis in Python. Scales to >100M cells.☆2,464Updated this week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- CellRank: dynamics from multi-view single-cell data☆449May 4, 2026Updated 2 weeks ago
- Automated, probabilistic assignment of cell types in scRNA-seq data☆213Jan 9, 2023Updated 3 years ago
- ☆73Apr 17, 2024Updated 2 years ago
- Deep probabilistic analysis of single-cell and spatial omics data☆1,623May 14, 2026Updated last week
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆606Jun 26, 2025Updated 10 months ago
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆485Apr 5, 2024Updated 2 years ago
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆225Apr 26, 2026Updated 3 weeks ago
- RNA velocity estimation in R☆197Sep 14, 2023Updated 2 years ago
- ☆284Oct 13, 2025Updated 7 months 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.
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆783Jan 6, 2024Updated 2 years ago
- Reference mapping for single-cell genomics☆404Mar 21, 2026Updated 2 months ago
- Imputation method for scRNA-seq based on low-rank approximation☆80Dec 14, 2023Updated 2 years ago
- URD - Reconstruction of Branching Developmental Trajectories☆127Jun 29, 2021Updated 4 years ago
- An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.☆174Jan 26, 2024Updated 2 years ago
- ☆452May 5, 2026Updated 2 weeks ago
- MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …☆381Oct 3, 2024Updated last year
- A package to help convert different single-cell data formats to each other☆465Feb 20, 2026Updated 3 months ago
- Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕☆185Jun 24, 2021Updated 4 years ago
- AI Agents on 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.
- Geometry-preserving random sampling☆97Oct 29, 2024Updated last year
- R package for integrating and analyzing multiple single-cell datasets☆429Feb 4, 2026Updated 3 months ago
- netNMF-sc: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data☆23Apr 19, 2021Updated 5 years ago
- Detect doublets in single-cell RNA-seq data☆86Jul 3, 2019Updated 6 years ago
- CytoSPACE: Optimal mapping of scRNA-seq data to spatial transcriptomics data☆143Feb 20, 2025Updated last year
- R package implementation of Milo for testing for differential abundance in KNN graphs☆432May 11, 2026Updated last week
- Single-cell RNA-seq Gene Expression Recovery☆114Nov 28, 2024Updated last year