Benchmarking gene embeddings on single, paired, and gene set tasks
☆23Nov 29, 2025Updated 9 months ago
Alternatives and similar repositories for gene-embedding-benchmarks
Users that are interested in gene-embedding-benchmarks are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆22Sep 19, 2025Updated last year
- ☆11Feb 21, 2023Updated 3 years ago
- ☆16Dec 8, 2025Updated 9 months ago
- Leveraging protein-language models for virtual screening☆27Jun 5, 2024Updated 2 years ago
- Embeddings to Network Alignment - align biological networks between two species☆10Sep 8, 2023Updated 3 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- A Python toolkit for setting up benchmarking dataset using biomedical networks☆22Aug 31, 2026Updated 3 weeks ago
- Bencharking pipeline for evaluating Transcriptomic representations for perturbation tasks☆16Nov 5, 2024Updated last year
- Integrate Any Omics: Towards genome-wide data integration for patient stratification☆62May 19, 2025Updated last year
- pytorch dataloaders for single-cell perturbation data☆54Jul 18, 2026Updated 2 months ago
- Data, results, and code accompanying the manuscript: "Supervised learning is an accurate method for network-based gene classification"☆10Nov 3, 2021Updated 4 years ago
- A repository for reproducing experiments from the TxPert paper☆51Mar 25, 2026Updated 5 months ago
- Get, parse, and extract information from the SRA metadata files☆46Sep 20, 2022Updated 4 years ago
- FunctionaL Omics Processing platform☆13Jul 25, 2024Updated 2 years ago
- ☆42Aug 19, 2026Updated last month
- 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.
- ☆53Jun 16, 2025Updated last year
- PLMSearch enables accurate and fast homologous protein search with only sequences as input☆82Sep 9, 2025Updated last year
- A simulation engine for compartmental models☆17Sep 4, 2026Updated 2 weeks ago
- CGMega: dissecting cancer gene module with explainable graph attention network☆19Jul 27, 2026Updated last month
- A Cellular Regulatory Network-Aware Transcriptomics Foundation Model☆38Dec 18, 2025Updated 9 months ago
- COCONUT (COlleCtion of Open Natural prodUcTs): A comprehensive platform facilitating natural product research by providing data, tools, a…☆66Jun 23, 2026Updated 3 months ago
- Diverse sampling for single-cell datasets☆17Mar 22, 2026Updated 6 months ago
- cz-benchmarks is a package for standardized evaluation and comparison of machine learning models for biological applications.☆57Dec 19, 2025Updated 9 months ago
- Collection of cloud-based biomedical data science learning modules funded by the National Institute of General Medical Sciences at the NI…☆94Jun 6, 2025Updated last year
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Pipeline to run scE2G☆65Sep 1, 2026Updated 3 weeks ago
- Chat offline with open-source LLMs like deepseek-r1, nemotron, qwen, llama and more all through a simple R package powered by Shiny and O…☆22Mar 12, 2025Updated last year
- SignalingProfiler is a pipeline that builds signaling networks to cellular phenotypes from multiomics data.☆15Mar 26, 2026Updated 5 months ago
- MATLAB implementation of Gene Set Enrichment Analysis (GSEA) method for finding pathways which can show more complex relation between cha…☆10Sep 7, 2022Updated 4 years ago
- Code and data for Cell-o1.☆29Jul 22, 2026Updated 2 months ago
- Public Codebase supporting the paper "Modeling Cellular Perturbations with The Sparse Additive Mechanism Shift Variational Autoencoder" b…☆17Oct 20, 2023Updated 2 years ago
- Python package for biodatafuse project.☆15Apr 22, 2026Updated 5 months ago
- Python library for converting between BioNLP formats☆23Apr 20, 2023Updated 3 years ago
- DomainMapper is a parser for hmmscan full output files built centrally around ECOD domain definitions. Users can optimize DomainMapper's …☆13Dec 13, 2023Updated 2 years ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Machine learning methods for spatially resolved transcriptomics with histology images: a collection of related resources.☆10Mar 22, 2022Updated 4 years ago
- ☆12Nov 24, 2022Updated 3 years ago
- Size-Wise Analysis of Transfer Learning of pLM Embeddings☆13Jun 10, 2025Updated last year
- ☆23Sep 27, 2019Updated 6 years ago
- ☆28May 22, 2025Updated last year
- A statistical tool to detect differential alternative splicing events using single-cell RNA-seq☆22Jul 31, 2023Updated 3 years ago
- ☆17Feb 27, 2026Updated 6 months ago