☆35Mar 5, 2026Updated this week
Alternatives and similar repositories for openpipeline
Users that are interested in openpipeline are comparing it to the libraries listed below
Sorting:
- script + metadata = standalone component☆45Updated this week
- Automatically annotate cell types, consistently across samples.☆19Updated this week
- R package for normalisation of spatial transcriptomics data☆17Jan 21, 2026Updated last month
- Multi-modal single cell analysis pipelines☆62Dec 11, 2025Updated 2 months ago
- A modular tool for proportion analysis in single-cell sequencing data☆24Feb 26, 2026Updated last week
- Formalizing and benchmarking open problems in single-cell genomics☆57Jun 11, 2025Updated 8 months ago
- Sample representation benchmark for single-cell data☆13Aug 11, 2025Updated 6 months ago
- Comprehensive pipeline for donor demultiplexing in single cell☆25Feb 28, 2026Updated last week
- We describe a transcriptional reference map of human natural killer (NK) cells based on analysis of scRNA-seq data from both blood and ti…☆14Oct 7, 2024Updated last year
- Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data☆113Updated this week
- The Single-Cell Pathology Landscape of Breast Cancer☆27Jan 14, 2020Updated 6 years ago
- Code and documentation for the curation of cellxgene datasets☆53Updated this week
- ☆13Apr 17, 2025Updated 10 months ago
- cell type specific, trait-associated gene regulation☆29Mar 31, 2025Updated 11 months ago
- Developmental Spatiotemporal Optimal Transport☆13Mar 19, 2025Updated 11 months ago
- RA Synovial Single-cell Multimodal Cell Atlas☆19Mar 6, 2024Updated 2 years ago
- a dataloader to work with large single cell datasets from lamindb☆36Feb 19, 2026Updated 2 weeks ago
- Multimodal Data (.h5mu) implementation for Python☆109Updated this week
- Python package to interactively annotate histological images within a jupyter notebook☆18Oct 20, 2025Updated 4 months ago
- Rust Backend for PyRanges Operations. More featureful and much faster replacement for the NCLS library☆30Feb 15, 2026Updated 2 weeks ago
- Weakly supervised learning uncovers phenotypic signatures in single-cell data☆38Dec 17, 2025Updated 2 months ago
- A python implementation of scran computeSumFactors: normalization by deconvolution for single-cell RNA-sequencing☆34Nov 4, 2023Updated 2 years ago
- ☆46Jan 28, 2026Updated last month
- Trends in single cell papers☆17Sep 23, 2024Updated last year
- A python package for Multiomics and Ecological Spatial Analysis (MESA)☆25Apr 8, 2025Updated 10 months ago
- Tutorials for learning scverse☆19Feb 23, 2026Updated last week
- A lightweight reimplementation of some of the algorithms in the MEME suite in Python.☆28Feb 22, 2026Updated last week
- Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.☆38Jan 22, 2026Updated last month
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆76Nov 2, 2025Updated 4 months ago
- Variance stabilizing transformation for Gamma Poisson distributed data☆22Apr 11, 2023Updated 2 years ago
- ☆24Oct 1, 2025Updated 5 months ago
- Detecting Aberrant Splicing Events from RNA-sequencing data☆16Dec 10, 2024Updated last year
- ☆25Dec 5, 2025Updated 3 months ago
- STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)☆117Apr 26, 2025Updated 10 months ago
- UniverSC: a flexible cross-platform single-cell data processing pipeline☆46Feb 25, 2024Updated 2 years ago
- Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many othe…☆120Feb 27, 2026Updated last week
- Visualising data frames as funky heatmaps 📊☆193Dec 12, 2025Updated 2 months ago
- A toolking for cell type hierarchies: marker selection & consistent classification☆22Nov 26, 2023Updated 2 years ago
- Genomic Features in Python from BioConductor's AnnotationHub☆22Feb 23, 2026Updated last week