Benchmarking analysis of data integration tools
☆408Sep 17, 2025Updated 6 months ago
Alternatives and similar repositories for scib
Users that are interested in scib are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆82Jan 23, 2025Updated last year
- Reference mapping for single-cell genomics☆400Dec 2, 2025Updated 3 months ago
- CellRank: dynamics from multi-view single-cell data☆433Mar 9, 2026Updated 2 weeks ago
- Additional code and analysis from the single-cell integration benchmarking project☆71Dec 19, 2022Updated 3 years ago
- A package to help convert different single-cell data formats to each other☆460Feb 20, 2026Updated last month
- Panoramic stitching of single cell data☆297Jul 14, 2025Updated 8 months ago
- Deep probabilistic analysis of single-cell and spatial omics data☆1,585Updated this week
- A tool for semi-automatic cell type classification☆459Mar 13, 2026Updated last week
- A Bayesian model for compositional single-cell data analysis☆193Jan 13, 2026Updated 2 months ago
- Accelerated, Python-only, single-cell integration benchmarking metrics☆89Updated this week
- data and model repository for single-cell data☆136Dec 21, 2023Updated 2 years ago
- Single-cell analysis in Python. Scales to >100M cells.☆2,379Updated this week
- R package implementation of Milo for testing for differential abundance in KNN graphs☆423Sep 4, 2025Updated 6 months ago
- Formalizing and benchmarking open problems in single-cell genomics☆424Nov 26, 2025Updated 3 months ago
- RNA Velocity generalized through dynamical modeling☆494Feb 25, 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…☆1,559Dec 11, 2022Updated 3 years ago
- R package for integrating and analyzing multiple single-cell datasets☆427Feb 4, 2026Updated last month
- A scanpy extension to analyse single-cell TCR and BCR data.☆246Mar 16, 2026Updated last week
- Differential expression analysis for single-cell RNA-seq data.☆206Oct 21, 2025Updated 5 months ago
- https://www.sc-best-practices.org☆1,170Mar 9, 2026Updated 2 weeks ago
- LIANA+: an all-in-one framework for cell-cell communication☆276Jan 24, 2026Updated last month
- LIANA: a LIgand-receptor ANalysis frAmework☆234Aug 7, 2024Updated last year
- muon is a multimodal omics Python framework☆264Jan 19, 2026Updated 2 months ago
- Convert between AnnData and SingleCellExperiment☆147Updated this week
- Single-cell perturbation analysis☆295Mar 16, 2026Updated last week
- Fast, sensitive and accurate integration of single-cell data with Harmony☆625Oct 10, 2025Updated 5 months ago
- Single cell trajectory detection☆298Feb 14, 2026Updated last month
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆181Mar 27, 2025Updated 11 months ago
- Single-cell Lung Cancer Atlas with 1.2M cells☆90Jan 19, 2025Updated last year
- Single cell perturbation prediction☆337Dec 5, 2024Updated last year
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆422Updated this week
- An interactive explorer for single-cell transcriptomics data☆756Updated this week
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆448Feb 18, 2025Updated last year
- Spatial Single Cell Analysis in Python☆555Mar 16, 2026Updated last week
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,678Mar 9, 2026Updated 2 weeks ago
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …☆488Updated this week
- ☆361Dec 9, 2021Updated 4 years ago
- Graph-linked unified embedding for single-cell multi-omics data integration☆456Feb 9, 2026Updated last month
- 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