Benchmarking analysis of data integration tools
☆407Sep 17, 2025Updated 5 months ago
Alternatives and similar repositories for scib
Users that are interested in scib are comparing it to the libraries listed below
Sorting:
- Reference mapping for single-cell genomics☆399Dec 2, 2025Updated 3 months ago
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆81Jan 23, 2025Updated last year
- CellRank: dynamics from multi-view single-cell data☆430Updated this week
- A package to help convert different single-cell data formats to each other☆458Feb 20, 2026Updated last week
- Additional code and analysis from the single-cell integration benchmarking project☆71Dec 19, 2022Updated 3 years ago
- A tool for semi-automatic cell type classification☆453Updated this week
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated 7 months ago
- Deep probabilistic analysis of single-cell and spatial omics data☆1,573Updated this week
- A Bayesian model for compositional single-cell data analysis☆188Jan 13, 2026Updated last month
- RNA Velocity generalized through dynamical modeling☆488Updated this week
- data and model repository for single-cell data☆136Dec 21, 2023Updated 2 years ago
- Formalizing and benchmarking open problems in single-cell genomics☆420Nov 26, 2025Updated 3 months ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆421Sep 4, 2025Updated 5 months ago
- Single-cell analysis in Python. Scales to >100M cells.☆2,359Updated this week
- R package for integrating and analyzing multiple single-cell datasets☆424Feb 4, 2026Updated 3 weeks ago
- Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…☆1,553Dec 11, 2022Updated 3 years ago
- Accelerated, Python-only, single-cell integration benchmarking metrics☆86Feb 24, 2026Updated last week
- A scanpy extension to analyse single-cell TCR and BCR data.☆245Feb 23, 2026Updated last week
- muon is a multimodal omics Python framework☆262Jan 19, 2026Updated last month
- LIANA+: an all-in-one framework for cell-cell communication☆271Jan 24, 2026Updated last month
- Differential expression analysis for single-cell RNA-seq data.☆206Oct 21, 2025Updated 4 months ago
- LIANA: a LIgand-receptor ANalysis frAmework☆232Aug 7, 2024Updated last year
- Single-cell perturbation analysis☆289Feb 23, 2026Updated last week
- Single cell perturbation prediction☆335Dec 5, 2024Updated last year
- https://www.sc-best-practices.org☆1,152Updated this week
- ☆360Dec 9, 2021Updated 4 years ago
- Convert between AnnData and SingleCellExperiment☆144Updated this week
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …☆489Feb 20, 2026Updated last week
- Fast, sensitive and accurate integration of single-cell data with Harmony☆622Oct 10, 2025Updated 4 months ago
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆416Feb 23, 2026Updated last week
- An interactive explorer for single-cell transcriptomics data☆755Updated this week
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,659Feb 15, 2026Updated 2 weeks ago
- This is the alpha version of the CellOracle package☆422Feb 3, 2026Updated last month
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆447Feb 18, 2025Updated last year
- Single-cell Lung Cancer Atlas with 1.2M cells☆87Jan 19, 2025Updated last year
- Spatial Single Cell Analysis in Python☆553Updated this week
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆118Jan 22, 2024Updated 2 years ago
- Episcanpy: Epigenomics Single Cell Analysis in Python☆150Dec 5, 2024Updated last year
- Graph-linked unified embedding for single-cell multi-omics data integration☆455Feb 9, 2026Updated 3 weeks ago