R toolkit for single cell genomics
☆2,707Apr 17, 2026Updated this week
Alternatives and similar repositories for seurat
Users that are interested in seurat are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,709Updated this week
- Single-cell analysis in Python. Scales to >100M cells.☆2,420Updated this week
- Fast, sensitive and accurate integration of single-cell data with Harmony☆639Apr 9, 2026Updated last week
- R package for detecting doublets in single-cell RNA sequencing data☆540Mar 21, 2025Updated last year
- ☆446Jan 8, 2026Updated 3 months 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.
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆777Jan 6, 2024Updated 2 years ago
- Inferring CNV from Single-Cell RNA-Seq☆662Nov 14, 2025Updated 5 months ago
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆334Jul 28, 2020Updated 5 years ago
- Community-provided extensions to Seurat☆358Feb 17, 2026Updated 2 months ago
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆254Jan 10, 2026Updated 3 months ago
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆481Apr 5, 2024Updated 2 years ago
- R toolkit for the analysis of single-cell chromatin data☆412Updated this week
- ☆293Jul 15, 2022Updated 3 years ago
- Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…☆1,561Dec 11, 2022Updated 3 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- 10x Genomics Single Cell Analysis☆455Dec 10, 2025Updated 4 months ago
- R package for integrating and analyzing multiple single-cell datasets☆427Feb 4, 2026Updated 2 months ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆319Nov 1, 2022Updated 3 years ago
- NicheNet: predict active ligand-target links between interacting cells☆637Nov 12, 2025Updated 5 months ago
- RNA Velocity generalized through dynamical modeling☆496Feb 25, 2026Updated last month
- Deep probabilistic analysis of single-cell and spatial omics data☆1,597Apr 12, 2026Updated last week
- ☆361Dec 9, 2021Updated 4 years ago
- Clone of the Bioconductor repository for the SingleR package.☆200Apr 8, 2026Updated last week
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆327Apr 23, 2024Updated last year
- Wordpress hosting with auto-scaling - Free Trial • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆446Feb 18, 2025Updated last year
- A package to help convert different single-cell data formats to each other☆462Feb 20, 2026Updated last month
- A universal enrichment tool for interpreting omics data☆1,196Apr 12, 2026Updated last week
- High dimensional weighted gene co-expression network analysis☆469Mar 13, 2026Updated last month
- Analysis of single cell RNA-seq data course☆679Apr 11, 2022Updated 4 years ago
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆595Jun 26, 2025Updated 9 months ago
- R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.☆295Apr 9, 2026Updated last week
- R package implementation of Milo for testing for differential abundance in KNN graphs☆425Apr 8, 2026Updated last week
- A tool for semi-automatic cell type classification☆466Mar 21, 2026Updated 3 weeks 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.
- Tools and methods for analysis of single cell assay data in R☆262Oct 17, 2025Updated 6 months ago
- ☆607Mar 23, 2021Updated 5 years ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics☆580Mar 4, 2026Updated last month
- A Shiny web app for mapping datasets using Seurat v4☆144Nov 5, 2024Updated last year
- An interactive explorer for single-cell transcriptomics data☆761Updated this week
- Interfaces for HDF5-based Single Cell File Formats☆176Nov 4, 2023Updated 2 years ago
- RNA-seq aligner☆2,178Mar 18, 2025Updated last year