Snakemake pipeline that works with the scIB package to benchmark data integration methods.
☆83Jan 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. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Benchmarking analysis of data integration tools☆426Apr 27, 2026Updated 3 months ago
- Additional code and analysis from the single-cell integration benchmarking project☆74Dec 19, 2022Updated 3 years ago
- A pipeline for droplet-based single-cell RNA-seq and spot-based spatial transcriptomics data secondary analysis implemented in the drake …☆17Aug 27, 2025Updated 11 months ago
- Accelerated, Python-only, single-cell integration benchmarking metrics☆97Updated this week
- Blastocyst-like structures generated from human pluripotent stem cells☆13Sep 25, 2022Updated 3 years ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- 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 3 years ago
- Single Cell Pretrained Regulatory network INference from Transcripts☆11Sep 17, 2024Updated last year
- Reference mapping for single-cell genomics☆407Jun 26, 2026Updated last month
- Inferring gene co-expression networks from single cell gene expression data☆29Aug 5, 2022Updated 4 years ago
- Pipeline framework for iteratively and reproducibly building and evaluating single cell atlases☆74Jul 29, 2026Updated 2 weeks ago
- Code for a multimodal atlas of healthy and injured cell states and niches in the human kidney☆27Mar 7, 2024Updated 2 years ago
- A package to help convert different single-cell data formats to each other☆470Feb 20, 2026Updated 5 months ago
- Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets☆43Jul 20, 2025Updated last year
- Single-cell Lung Cancer Atlas with 1.2M cells☆94Jan 19, 2025Updated last year
- 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 Bayesian model for compositional single-cell data analysis☆199Jan 13, 2026Updated 7 months ago
- LIANA: a LIgand-receptor ANalysis frAmework☆247Aug 7, 2024Updated 2 years ago
- Shiny app for the analysis of single cell data☆26Jun 20, 2026Updated last month
- Automated cell type classification☆116Jan 3, 2025Updated last year
- reticulate-free single cell format conversion☆219Jul 10, 2026Updated last month
- Coarse-graining of large single-cell RNA-seq data into metacells☆105Apr 16, 2026Updated 3 months ago
- A tool for semi-automatic cell type harmonization and integration☆121Mar 9, 2026Updated 5 months ago
- Port of symphony algorithm of single-cell reference atlas mapping to Python☆34May 19, 2026Updated 2 months ago
- Memory-efficient single-cell analysis in Python. Stream RNA, ATAC, CITE-seq and multi-omics from local or remote Zarr stores, from laptop…☆122Updated this week
- 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.
- A tool for semi-automatic cell type classification☆500May 22, 2026Updated 2 months ago
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆195Aug 12, 2025Updated last year
- Gene set scoring for single-cell data☆204Apr 29, 2026Updated 3 months ago
- Supplementary files and notebooks to recreate figures.☆23Aug 4, 2026Updated last week
- ☆16May 23, 2022Updated 4 years ago
- ☆132Jul 11, 2026Updated last month
- ☆48Apr 18, 2020Updated 6 years ago
- This repository contains code for the evaluation of epithelial-to-mesenchymal transition states in cancer.☆13Jan 24, 2023Updated 3 years ago
- Easy single cell analysis platform for enrichment☆228Updated this week
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- CellRank: dynamics from multi-view single-cell data☆454Aug 3, 2026Updated last week
- single-cell analysis workflows for double phosphoramidite barcode and UMI Correction (scCOLOR-seq)☆13Jul 13, 2023Updated 3 years ago
- Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…☆1,584Dec 11, 2022Updated 3 years ago
- R package for pathway analysis in scRNA-seq data☆82Aug 17, 2024Updated last year
- R package implementation of Milo for testing for differential abundance in KNN graphs☆442May 11, 2026Updated 3 months ago
- An R implementation of the Gene Frequency - Inverse Cell Frequency method for single cell data normalization☆20Aug 29, 2023Updated 2 years ago
- SPATA Package for spatial gene expression analysis☆21May 6, 2022Updated 4 years ago