clinicalml / sc-foundation-evalLinks
Code for evaluating single cell foundation models scBERT and scGPT
☆46Updated 11 months ago
Alternatives and similar repositories for sc-foundation-eval
Users that are interested in sc-foundation-eval are comparing it to the libraries listed below
Sorting:
- Codes for paper: Evaluating the Utilities of Large Language Models in Single-cell Data Analysis.☆72Updated 2 months ago
- Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.☆61Updated last year
- scPerturb: A resource and a python/R tool for single-cell perturbation data☆138Updated 6 months ago
- Transformer for One-Stop Interpretable Cell-type Annotation☆144Updated last year
- single cell foundation model☆97Updated this week
- A simulator for single cell multi-omics and spatial omics data that provides ground truth to benchmark a wide range of methods.☆59Updated 7 months ago
- ☆133Updated last year
- Repository for Nicheformer: a foundation model for single-cell and spatial omics☆95Updated 5 months ago
- ☆81Updated last year
- Single-cell biological network inference using a heterogeneous graph transformer☆73Updated 6 months ago
- ☆53Updated 8 months ago
- End-to-end analysis of spatial multi-omics data☆90Updated 2 weeks ago
- The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell leve…☆109Updated last year
- A unified approach for integrating spatial and single-cell transcriptomics data by leveraging deep generative models☆69Updated last year
- Single-Cell (Perturbation) Model Library☆66Updated 3 weeks ago
- ☆59Updated 11 months ago
- Modeling complex perturbations with CellFlow☆82Updated this week
- Additional code and analysis from the single-cell integration benchmarking project☆66Updated 2 years ago
- A model developed for the generation of scRNA-seq data☆68Updated 6 months ago
- Models and datasets for perturbational single-cell omics☆161Updated 3 years ago
- Accelerated, Python-only, single-cell integration benchmarking metrics☆67Updated last week
- PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).☆60Updated last week
- SIMBA: SIngle-cell eMBedding Along with features☆63Updated 10 months ago
- Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.☆98Updated 7 months ago
- Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.☆27Updated 3 weeks ago
- GeneCompass☆86Updated 2 months ago
- ☆50Updated 5 months ago
- ☆47Updated last month
- ☆36Updated 2 months ago
- scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics☆103Updated 5 months ago