YosefLab / scib-metrics
Accelerated, Python-only, single-cell integration benchmarking metrics
☆56Updated this week
Alternatives and similar repositories for scib-metrics:
Users that are interested in scib-metrics are comparing it to the libraries listed below
- Additional code and analysis from the single-cell integration benchmarking project☆59Updated 2 years ago
- Python implementation of Milo for differential abundance testing on KNN graph☆64Updated last month
- Multi-omic velocity inference☆110Updated 5 months ago
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆110Updated last year
- End-to-end analysis of spatial multi-omics data☆65Updated 3 weeks ago
- A python port of the R package SCTransform:☆19Updated 3 years ago
- spatial transcriptome, single cell☆67Updated 2 years ago
- Metacells - Single-cell RNA Sequencing Analysis☆104Updated 6 months ago
- scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics☆93Updated last month
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆61Updated 11 months ago
- Code used to benchmark Xenium☆56Updated 9 months ago
- ☆72Updated this week
- Predict RNA velocity through deep learning☆67Updated last year
- Single cell omics biology annotations☆51Updated last month
- scPerturb: A resource and a python/R tool for single-cell perturbation data☆119Updated last month
- ☆30Updated last week
- ☆51Updated last week
- Awesome list of tools and methods to perform spatial transcriptomic data analysis.☆40Updated 3 years ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆59Updated 10 months ago
- ☆46Updated last week
- Unsupervised Deep Disentangled Representation of Single-Cell Omics☆39Updated this week
- CZ CELLxGENE Discover Census☆98Updated last week
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆69Updated 2 months ago
- A tool for semi-automatic cell type harmonization and integration☆102Updated 3 weeks ago
- This repository contains all code used for the Human Lung Cell Atlas project.☆49Updated last year
- ☆45Updated 2 years ago
- Formalizing and benchmarking open problems in single-cell genomics☆56Updated 4 months ago
- Multi-omic single-cell optimal transport tools☆150Updated this week
- ☆47Updated last year
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆71Updated 3 weeks ago