Benchmarking analysis of data integration tools
☆435Apr 27, 2026Updated 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.☆85Jan 23, 2025Updated last year
- Reference mapping for single-cell genomics☆414Jun 26, 2026Updated 4 months ago
- CellRank: dynamics from multi-view single-cell data☆459Oct 14, 2026Updated 2 weeks ago
- Deep probabilistic analysis of single-cell and spatial omics data☆1,720Updated this week
- A package to help convert different single-cell data formats to each other☆471Feb 20, 2026Updated 8 months ago
- 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.
- Additional code and analysis from the single-cell integration benchmarking project☆76Dec 19, 2022Updated 3 years ago
- Accelerated, Python-only, single-cell integration benchmarking metrics☆98Updated this week
- A tool for semi-automatic cell type classification☆517May 22, 2026Updated 5 months ago
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated last year
- R package for integrating and analyzing multiple single-cell datasets☆435Aug 18, 2026Updated 2 months ago
- Single-cell analysis in Python. Scales to >100M cells.☆2,604Updated this week
- R package implementation of Milo for testing for differential abundance in KNN graphs☆450Aug 25, 2026Updated 2 months ago
- https://www.sc-best-practices.org☆1,295Updated this week
- RNA Velocity generalized through dynamical modeling☆514Feb 25, 2026Updated 8 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- LIANA+: an all-in-one framework for cell-cell communication☆325Updated this week
- A Bayesian model for compositional single-cell data analysis☆204Jan 13, 2026Updated 9 months ago
- This is the alpha version of the CellOracle package☆508Apr 30, 2026Updated 6 months ago
- Formalizing and benchmarking open problems in single-cell genomics☆445Oct 2, 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…☆1,599Dec 11, 2022Updated 3 years ago
- Single cell perturbation prediction☆361Dec 5, 2024Updated last year
- data and model repository for single-cell data☆135Dec 21, 2023Updated 2 years ago
- A scanpy extension to analyse single-cell TCR and BCR data.☆268Updated this week
- Convert between AnnData and SingleCellExperiment☆154Updated this week
- Proton VPN Special Offer - Get 70% off • AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Single-cell perturbation analysis☆355Updated this week
- Single cell trajectory detection☆345Sep 23, 2026Updated last month
- Fast, sensitive and accurate integration of single-cell data with Harmony☆676Oct 15, 2026Updated 2 weeks ago
- Differential expression analysis for single-cell RNA-seq data.☆204Oct 21, 2025Updated last year
- muon is a multimodal omics Python framework☆279Updated this week
- SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data☆203Aug 24, 2026Updated 2 months ago
- Python package to perform enrichment analysis from omics data.☆301Updated this week
- Spatial Single Cell Analysis in Python☆612Updated this week
- Graph-linked unified embedding for single-cell multi-omics data integration☆483Feb 9, 2026Updated 8 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.
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,888Updated this week
- ☆1,662Apr 29, 2026Updated 6 months ago
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction …☆511Oct 15, 2026Updated 2 weeks ago
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆427Sep 12, 2026Updated last month
- Methods for detecting doublets in single-cell sequencing data☆276Oct 18, 2026Updated last week
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆465Oct 19, 2026Updated last week
- LIANA: a LIgand-receptor ANalysis frAmework☆253Aug 7, 2024Updated 2 years ago