☆93Aug 18, 2025Updated 6 months ago
Alternatives and similar repositories for geneformer
Users that are interested in geneformer are comparing it to the libraries listed below
Sorting:
- ☆391Nov 23, 2025Updated 3 months ago
- 🏃 The go-to single-cell Foundation Model☆142Feb 20, 2026Updated last week
- Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.☆62May 30, 2024Updated last year
- ☆1,481Nov 12, 2025Updated 3 months ago
- Bencharking pipeline for evaluating Transcriptomic representations for perturbation tasks☆12Nov 5, 2024Updated last year
- ☆347Dec 13, 2023Updated 2 years ago
- GeneCompass☆111Feb 10, 2026Updated 2 weeks ago
- ☆11May 14, 2025Updated 9 months ago
- A single-cell RNA-seq data generative model☆18Jan 11, 2025Updated last year
- Comprehensive suite for evaluating perturbation prediction models☆122Updated this week
- ☆407Jan 21, 2026Updated last month
- ☆34Jun 7, 2019Updated 6 years ago
- ☆18Jul 30, 2022Updated 3 years ago
- Codes for paper: Evaluating the Utilities of Large Language Models in Single-cell Data Analysis.☆108Feb 4, 2026Updated 3 weeks ago
- ☆15Nov 3, 2025Updated 3 months ago
- Run multiple Pipeline5 instances at once☆11Jun 6, 2025Updated 8 months ago
- Code for "LangCell: Language-Cell Pre-training for Cell Identity Understanding".☆65Dec 29, 2024Updated last year
- Simple pure Python SAM parser and objects for working with SAM records☆64Jun 21, 2022Updated 3 years ago
- Repository for Nicheformer: a foundation model for single-cell and spatial omics☆151Nov 23, 2025Updated 3 months ago
- Public repo for rbio, a biologically-informed reasoning model trained on virtual cell models as verifiers☆133Nov 24, 2025Updated 3 months ago
- ☆17May 23, 2025Updated 9 months ago
- stageR package☆13Feb 28, 2023Updated 3 years ago
- ☆11May 6, 2021Updated 4 years ago
- Shell bootloader for data science.☆12Feb 22, 2026Updated last week
- ☆10Oct 15, 2025Updated 4 months ago
- ☆310Mar 18, 2024Updated last year
- Seamless navigation through combined results of set-based and network-based enrichment analysis☆22Sep 14, 2025Updated 5 months ago
- Single-Cell Multimodal Prediction via Transformer☆28Feb 7, 2024Updated 2 years ago
- ☆79Jan 9, 2026Updated last month
- State is a machine learning model that predicts cellular perturbation response across diverse contexts☆522Updated this week
- [ICCAD 2025] Squant☆15Jul 3, 2025Updated 7 months ago
- ☆13Jun 4, 2023Updated 2 years ago
- ☆16Mar 3, 2023Updated 2 years ago
- SClineager: a Bayesian hierarchical model that performs lineage tracing of single cells based on genetic markers☆10Apr 30, 2024Updated last year
- Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.☆36Jul 29, 2025Updated 7 months ago
- Extracts fastq reads for specified barcode(s) from one or multiple FASTQ files☆13Jan 31, 2016Updated 10 years ago
- An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data☆13Jul 2, 2024Updated last year
- [NeurIPS 2024] "NovoBench: Benchmarking Deep Learning-based \emph{De Novo} Sequencing Methods in Proteomics"☆12Nov 23, 2024Updated last year
- Stack is a single-cell foundation model that enables in-context learning at inference time.☆87Jan 30, 2026Updated last month