Snakemake pipeline that works with the scIB package to benchmark data integration methods.
☆82Jan 23, 2025Updated last year
Alternatives and similar repositories for scib-pipeline
Users that are interested in scib-pipeline are comparing it to the libraries listed below
Sorting:
- Benchmarking analysis of data integration tools☆408Sep 17, 2025Updated 5 months ago
- Additional code and analysis from the single-cell integration benchmarking project☆71Dec 19, 2022Updated 3 years ago
- GIANT (Gene-based data Integration and ANalysis Technique) is a method for large-scale joint analyses of atlas-level single cell data.☆14Jun 13, 2023Updated 2 years ago
- A pipeline for droplet-based single-cell RNA-seq and spot-based spatial transcriptomics data secondary analysis implemented in the drake …☆15Aug 27, 2025Updated 6 months ago
- Reference mapping for single-cell genomics☆400Dec 2, 2025Updated 3 months ago
- Accelerated, Python-only, single-cell integration benchmarking metrics☆87Mar 2, 2026Updated last week
- Single-cell Lung Cancer Atlas with 1.2M cells☆87Jan 19, 2025Updated last year
- Single Cell Pretrained Regulatory network INference from Transcripts☆11Sep 17, 2024Updated last year
- Blastocyst-like structures generated from human pluripotent stem cells☆13Sep 25, 2022Updated 3 years ago
- A Bayesian model for compositional single-cell data analysis☆191Jan 13, 2026Updated last month
- Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets☆42Jul 20, 2025Updated 7 months ago
- ☆16May 23, 2022Updated 3 years ago
- This repository contains code for the evaluation of epithelial-to-mesenchymal transition states in cancer.☆13Jan 24, 2023Updated 3 years ago
- single-cell analysis workflows for double phosphoramidite barcode and UMI Correction (scCOLOR-seq)☆13Jul 13, 2023Updated 2 years ago
- Code for EpiMap data browser☆14Jun 4, 2024Updated last year
- ☆13Aug 9, 2022Updated 3 years ago
- A package to help convert different single-cell data formats to each other☆458Feb 20, 2026Updated 2 weeks ago
- CellRank: dynamics from multi-view single-cell data☆431Updated this week
- LIANA: a LIgand-receptor ANalysis frAmework☆233Aug 7, 2024Updated last year
- Inferring gene co-expression networks from single cell gene expression data☆28Aug 5, 2022Updated 3 years ago
- Shiny app for the analysis of single cell data☆26Nov 11, 2025Updated 3 months ago
- Coarse-graining of large single-cell RNA-seq data into metacells☆96Feb 23, 2026Updated 2 weeks ago
- A tool for semi-automatic cell type classification☆457Mar 1, 2026Updated last week
- ☆50Nov 28, 2025Updated 3 months ago
- ☆47Apr 18, 2020Updated 5 years ago
- A tool for semi-automatic cell type harmonization and integration☆118Nov 3, 2025Updated 4 months ago
- Analysis of imbalanced data and its impacts in a scRNA-seq integration setting☆31Mar 7, 2025Updated last year
- Automated cell type classification☆116Jan 3, 2025Updated last year
- Port of symphony algorithm of single-cell reference atlas mapping to Python☆34Dec 11, 2025Updated 2 months ago
- RNA Velocity generalized through dynamical modeling☆491Feb 25, 2026Updated last week
- Supplementary files and notebooks to recreate figures.☆21Aug 12, 2025Updated 6 months ago
- Reworked clustering metrics for assessing performance in imbalanced settings☆18Jun 3, 2024Updated last year
- Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with mill…☆114Nov 19, 2025Updated 3 months ago
- A scalable SCENIC workflow for single-cell gene regulatory network analysis☆174Dec 8, 2022Updated 3 years ago
- Various utility functions for Seurat v5 single-cell analysis☆63Feb 20, 2026Updated 2 weeks ago
- ☆46May 17, 2022Updated 3 years ago
- Gene set scoring for single-cell data☆184Feb 11, 2026Updated 3 weeks ago
- ☆18Oct 4, 2022Updated 3 years ago
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆182Aug 12, 2025Updated 6 months ago