Reference mapping for single-cell genomics
☆411Jun 26, 2026Updated 2 months ago
Alternatives and similar repositories for scarches
Users that are interested in scarches are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- CellRank: dynamics from multi-view single-cell data☆456Sep 16, 2026Updated last week
- Benchmarking analysis of data integration tools☆432Apr 27, 2026Updated 4 months ago
- RNA Velocity generalized through dynamical modeling☆512Feb 25, 2026Updated 6 months ago
- Deep probabilistic analysis of single-cell and spatial omics data☆1,695Updated this week
- data and model repository for single-cell data☆136Dec 21, 2023Updated 2 years 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.
- A tool for semi-automatic cell type classification☆504May 22, 2026Updated 4 months ago
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated last year
- R package implementation of Milo for testing for differential abundance in KNN graphs☆448Aug 25, 2026Updated 3 weeks ago
- Single cell perturbation prediction☆356Dec 5, 2024Updated last year
- A Bayesian model for compositional single-cell data analysis☆203Jan 13, 2026Updated 8 months ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆423Sep 12, 2026Updated last week
- A package to help convert different single-cell data formats to each other☆470Feb 20, 2026Updated 7 months ago
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆199Aug 24, 2026Updated 3 weeks ago
- Efficient and precise single-cell reference atlas mapping with Symphony☆126May 24, 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.
- A scanpy extension to analyse single-cell TCR and BCR data.☆266Updated this week
- R package for integrating and analyzing multiple single-cell datasets☆432Aug 18, 2026Updated last month
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …☆510Jul 26, 2026Updated last month
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆639Jun 26, 2025Updated last year
- ☆363Dec 9, 2021Updated 4 years ago
- Conversion between scRNA-seq objects☆210May 5, 2026Updated 4 months ago
- NicheNet: predict active ligand-target links between interacting cells☆680Jun 1, 2026Updated 3 months ago
- Differential expression analysis for single-cell RNA-seq data.☆205Oct 21, 2025Updated 11 months ago
- MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …☆387Oct 3, 2024Updated last year
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Fast, sensitive and accurate integration of single-cell data with Harmony☆672Jun 5, 2026Updated 3 months ago
- Single-cell analysis in Python. Scales to >100M cells.☆2,565Updated this week
- This is the alpha version of the CellOracle package☆501Apr 30, 2026Updated 4 months ago
- muon is a multimodal omics Python framework☆280Updated this week
- Interpretation of cell states using reference single-cell maps☆326Dec 19, 2025Updated 9 months ago
- A toolkit for single-cell immune profiling☆376Aug 14, 2026Updated last month
- Spatial Single Cell Analysis in Python☆598Updated this week
- Single-cell perturbation analysis☆346Updated this week
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆461Aug 31, 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.
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆125Jan 22, 2024Updated 2 years ago
- Metacells - Single-cell RNA Sequencing Analysis☆130Sep 4, 2026Updated 2 weeks ago
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆470Apr 11, 2026Updated 5 months ago
- Single-cell Transcriptome and Regulome Analysis Pipeline☆312Mar 6, 2023Updated 3 years ago
- Formalizing and benchmarking open problems in single-cell genomics☆438Aug 18, 2026Updated last month
- Single cell trajectory detection☆336Jul 15, 2026Updated 2 months ago
- ☆39Apr 21, 2026Updated 5 months ago