Snakemake pipeline that works with the scIB package to benchmark data integration methods.
☆84Jan 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☆432Apr 27, 2026Updated 5 months ago
- Additional code and analysis from the single-cell integration benchmarking project☆75Dec 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 last year
- Accelerated, Python-only, single-cell integration benchmarking metrics☆97Oct 6, 2026Updated last week
- Blastocyst-like structures generated from human pluripotent stem cells☆13Sep 25, 2022Updated 4 years ago
- 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.
- 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 2 years ago
- Reference mapping for single-cell genomics☆412Jun 26, 2026Updated 3 months ago
- 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☆80Updated this week
- Visualizing Somatic Alterations of 10X Spatial Transcriptomics Data☆16Nov 7, 2024Updated last year
- 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☆471Feb 20, 2026Updated 7 months ago
- Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets☆43Jul 20, 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.
- Single-cell Lung Cancer Atlas with 1.2M cells☆94Jan 19, 2025Updated last year
- A Bayesian model for compositional single-cell data analysis☆203Jan 13, 2026Updated 9 months ago
- LIANA: a LIgand-receptor ANalysis frAmework☆252Aug 7, 2024Updated 2 years ago
- Shiny app for the analysis of single cell data☆26Jun 20, 2026Updated 3 months ago
- Automated cell type classification☆117Jan 3, 2025Updated last year
- reticulate-free single cell format conversion☆221Jul 10, 2026Updated 3 months ago
- A tool for semi-automatic cell type harmonization and integration☆123Mar 9, 2026Updated 7 months ago
- Coarse-graining of large single-cell RNA-seq data into metacells☆110Apr 16, 2026Updated 5 months ago
- Port of symphony algorithm of single-cell reference atlas mapping to Python☆34May 19, 2026Updated 4 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.
- Interactively analyze single cell genomic data☆190Updated this week
- Memory-efficient single-cell analysis in Python. Stream RNA, ATAC, CITE-seq and multi-omics from local or remote Zarr stores, from laptop…☆126Updated this week
- A tool for semi-automatic cell type classification☆510May 22, 2026Updated 4 months ago
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆202Aug 12, 2025Updated last year
- Gene set scoring for single-cell data☆212Sep 8, 2026Updated last month
- Supplementary files and notebooks to recreate figures.☆24Aug 4, 2026Updated 2 months ago
- ☆16May 23, 2022Updated 4 years ago
- ☆141Jul 11, 2026Updated 3 months ago
- ☆48Apr 18, 2020Updated 6 years ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- 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☆237Aug 9, 2026Updated 2 months ago
- CellRank: dynamics from multi-view single-cell data☆457Oct 5, 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…☆1,597Dec 11, 2022Updated 3 years ago
- R package for pathway analysis in scRNA-seq data☆81Aug 17, 2024Updated 2 years ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆450Aug 25, 2026Updated last month