Single cell perturbation prediction
☆335Dec 5, 2024Updated last year
Alternatives and similar repositories for scgen
Users that are interested in scgen are comparing it to the libraries listed below
Sorting:
- ☆33Oct 4, 2020Updated 5 years ago
- Reference mapping for single-cell genomics☆399Dec 2, 2025Updated 3 months ago
- Deep probabilistic analysis of single-cell and spatial omics data☆1,569Updated this week
- Deep count autoencoder for denoising scRNA-seq data☆269Mar 21, 2024Updated last year
- Models and datasets for perturbational single-cell omics☆172Aug 19, 2022Updated 3 years ago
- Single-cell analysis in Python. Scales to >100M cells.☆2,359Updated this week
- Panoramic stitching of single cell data☆295Jul 14, 2025Updated 7 months ago
- Benchmarking analysis of data integration tools☆407Sep 17, 2025Updated 5 months ago
- RNA Velocity generalized through dynamical modeling☆488Updated this week
- Batch balanced KNN☆178Oct 11, 2023Updated 2 years ago
- CellRank: dynamics from multi-view single-cell data☆430Updated this week
- Conditional out-of-distribution prediction☆62Aug 2, 2024Updated last year
- This is the alpha version of the CellOracle package☆421Feb 3, 2026Updated 3 weeks ago
- Quantifying experimental perturbations at single cell resolution☆113Sep 27, 2024Updated last year
- A package to help convert different single-cell data formats to each other☆458Feb 20, 2026Updated last week
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆579Jun 26, 2025Updated 8 months ago
- The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell leve…☆135Aug 14, 2024Updated last year
- Single-cell perturbation analysis☆289Feb 23, 2026Updated last week
- scPerturb: A resource and a python/R tool for single-cell perturbation data☆169Feb 25, 2025Updated last year
- Differential expression analysis for single-cell RNA-seq data.☆206Oct 21, 2025Updated 4 months ago
- MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …☆378Oct 3, 2024Updated last year
- Regulatory networks with Direct Information in python☆40Mar 9, 2023Updated 2 years ago
- Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)☆416Feb 23, 2026Updated last week
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆219Feb 26, 2024Updated 2 years ago
- A tool for semi-automatic cell type classification☆453Updated this week
- Spatial Single Cell Analysis in Python☆553Updated this week
- ☆360Dec 9, 2021Updated 4 years ago
- The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell lev…☆184Sep 7, 2023Updated 2 years ago
- data and model repository for single-cell data☆136Dec 21, 2023Updated 2 years ago
- Conversion between scRNA-seq objects☆200Jan 12, 2026Updated last month
- R package implementation of Milo for testing for differential abundance in KNN graphs☆420Sep 4, 2025Updated 5 months ago
- A Bayesian model for compositional single-cell data analysis☆188Jan 13, 2026Updated last month
- Learning Single-Cell Perturbation Responses using Neural Optimal Transport☆159Oct 31, 2024Updated last year
- muon is a multimodal omics Python framework☆262Jan 19, 2026Updated last month
- AUCell: score single cells with gene regulatory networks☆185Mar 9, 2024Updated last year
- CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.☆378Jul 30, 2025Updated 7 months ago
- NicheNet: predict active ligand-target links between interacting cells☆620Nov 12, 2025Updated 3 months ago
- software to detect doublets☆96Dec 28, 2024Updated last year
- Simple simulation of single-cell RNA sequencing data☆234Jan 12, 2026Updated last month