scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics
☆121Sep 29, 2025Updated 8 months ago
Alternatives and similar repositories for scDesign3
Users that are interested in scDesign3 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- A robust DE test method that accounts for the uncertainty in pseudotime inference☆40Mar 2, 2025Updated last year
- A post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping☆29Apr 5, 2026Updated 2 months ago
- An interpretable simulator that generates realistic single-cell gene expression count data with gene correlations recapitulated☆29Nov 2, 2024Updated last year
- A single cell sequencing read simulator.☆34Oct 14, 2024Updated last year
- Space- and time-optimal algorithms for large single-cell expression matrices, with a focus on single-cell CRISPR screens.☆13Updated this week
- 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.
- ESICCC: A systematic computational framework for evaluation, selection and integration of cell-cell communication inference methods☆13Jan 10, 2024Updated 2 years ago
- A clustering algorithm that can perform internal validation inspired by forest fire dynamics and self-organized criticality☆18May 18, 2022Updated 4 years ago
- From geospatial to spatial -omics☆103May 8, 2026Updated last month
- R package to infer biological activities from omics data using a collection of methods.☆297Dec 16, 2025Updated 5 months ago
- Data analysis for the moscot-framework project☆25Feb 27, 2026Updated 3 months ago
- AUCell: score single cells with gene regulatory networks☆195Mar 9, 2024Updated 2 years ago
- Multi-omic single-cell optimal transport tools☆212Updated this week
- Generate high quality, publication ready visualizations for single cell transcriptomics data.☆223Mar 2, 2026Updated 3 months ago
- This is the alpha version of the CellOracle package☆462Apr 30, 2026Updated last month
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- scPerturb: A resource and a python/R tool for single-cell perturbation data☆177Feb 25, 2025Updated last year
- R package for single cell and other data analysis using diffusion maps☆106Apr 15, 2026Updated 2 months ago
- A tool for semi-automatic cell type classification☆487May 22, 2026Updated 3 weeks ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆434May 11, 2026Updated last month
- ☆39Apr 16, 2025Updated last year
- A tool for detecting somatic variants in single cell data☆221Sep 15, 2024Updated last year
- Matilda is a multi-task framework for learning from single-cell multimodal omics data. Matilda leverages the information from the multi-m…☆22Jun 6, 2025Updated last year
- Coarse-graining of large single-cell RNA-seq data into metacells☆102Apr 16, 2026Updated last month
- Comparison of methods for trajectory inference on single-cell data 🥇☆222Aug 30, 2023Updated 2 years ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Code repository for macsGESTALT single cell lineage tracing analysis https://doi.org/10.1101/2020.08.11.245787☆10May 10, 2021Updated 5 years ago
- Convert your single-cell/spatial analyses to parallel HPC/cloud workflows just using pipes in R☆18May 19, 2026Updated 3 weeks ago
- ☆14Aug 13, 2023Updated 2 years ago
- SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) a…☆258Jan 16, 2026Updated 4 months ago
- Single-cell generalized trendmodel (scGTM): a flexible and interpretable model for gene expression along cell pseudotime. This is a Pyt…☆12Sep 26, 2023Updated 2 years ago
- ☆14Jan 24, 2024Updated 2 years ago
- LIANA: a LIgand-receptor ANalysis frAmework☆242Aug 7, 2024Updated last year
- An R package for visualising cell-cell interactions☆47Mar 16, 2026Updated 2 months ago
- Experimental design framework for scRNAseq population studies (eQTL and DE)☆49Jan 8, 2025Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Python library for plotting Cellphonedb results. Ported from ktplots R package.☆57May 29, 2026Updated 2 weeks ago
- Semi-supervised adversarial neural networks for classification of single cell transcriptomics data☆78Apr 4, 2026Updated 2 months ago
- Single-cell analysis with non-negative matrix factorization☆48Jul 24, 2025Updated 10 months ago
- scVI extension for unspliced RNA☆15May 18, 2025Updated last year
- Molecular interactions inference from single-cell multi-omics data☆31May 7, 2026Updated last month
- Causal inference, differential expression, and co-expression for scRNA-seq☆21Updated this week
- This contains the dataset for comparing scRNA-seq analysis methods☆94Aug 26, 2020Updated 5 years ago