Alternatives and similar repositories for geneformer

Users that are interested in geneformer are comparing it to the libraries listed below

• HelloWorldLTY / scEval
  Codes for paper: Evaluating the Utilities of Large Language Models in Single-cell Data Analysis.
  ☆71Updated 3 weeks ago
• theislab / CellFlow
  Modeling complex perturbations with CellFlow
  ☆64Updated this week
• xianglin226 / Benchmarking-Single-Cell-Perturbation
  Single-Cell (Perturbation) Model Library
  ☆63Updated 2 weeks ago
• theislab / nicheformer
  Repository for Nicheformer: a foundation model for single-cell and spatial omics
  ☆94Updated 3 months ago
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆129Updated 4 months ago
• snap-stanford / UCE
  UCE is a zero-shot foundation model for single-cell gene expression data
  ☆207Updated 4 months ago
• xCompass-AI / GeneCompass
  GeneCompass
  ☆84Updated 3 weeks ago
• OmicsML / CellPLM
  Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.
  ☆87Updated last year
• Perturbation-Response-Prediction / PRnet
  PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturb…
  ☆54Updated 7 months ago
• clinicalml / sc-foundation-eval
  Code for evaluating single cell foundation models scBERT and scGPT
  ☆44Updated 10 months ago
• SuperBianC / scMulan
  Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
  ☆58Updated last year
• PharMolix / LangCell
  Code for "LangCell: Language-Cell Pre-training for Cell Identity Understanding".
  ☆60Updated 6 months ago
• EperLuo / scDiffusion
  A model developed for the generation of scRNA-seq data
  ☆67Updated 4 months ago
• JackieHanLab / TOSICA
  Transformer for One-Stop Interpretable Cell-type Annotation
  ☆142Updated last year
• snap-stanford / SATURN
  ☆131Updated last year
• tianshilu / pMTnet
  Deep Learning the T Cell Receptor Binding Specificity of Neoantigen
  ☆82Updated 3 years ago
• microsoft / zero-shot-scfoundation
  ☆72Updated 10 months ago
• theislab / chemCPA
  Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
  ☆117Updated 5 months ago
• theislab / cpa
  The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell leve…
  ☆102Updated 11 months ago
• OmicsML / awesome-foundation-model-single-cell-papers
  ☆303Updated last week
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆153Updated 2 years ago
• biomed-AI / CellFM
  ☆61Updated last month
• snap-stanford / GEARS
  GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
  ☆272Updated 5 months ago
• carpenter-singh-lab / 2022_Haghighi_NatureMethods
  High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
  ☆48Updated 5 months ago
• welch-lab / PerturbNet
  PerturbNet is a deep generative model that can predict the distribution of cell states induced by chemical or genetic perturbation
  ☆34Updated this week
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆60Updated 3 months ago
• ZhangLabGT / scMultiSim
  A simulator for single cell multi-omics and spatial omics data that provides ground truth to benchmark a wide range of methods.
  ☆57Updated 6 months ago
• aaronwtr / PertEval
  Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.
  ☆26Updated 2 weeks ago
• ArcInstitute / state
  State is a machine learning model that predicts cellular perturbation response across diverse contexts
  ☆241Updated this week
• theislab / single-cell-transformer-papers
  ☆321Updated last month