Alternatives and similar repositories for awesome-single-cell-foundation

Users that are interested in awesome-single-cell-foundation are comparing it to the libraries listed below

• welch-lab / PerturbNet
  PerturbNet is a deep generative model that can predict the distribution of cell states induced by chemical or genetic perturbation
  ☆49Updated 2 months ago
• theislab / chemCPA
  Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
  ☆124Updated 8 months ago
• ArcInstitute / cell-eval
  Comprehensive suite for evaluating perturbation prediction models
  ☆89Updated last week
• yhr91 / GEARS_misc
  ☆22Updated 11 months ago
• OmicsML / scDiff
  scDiff: A General Single-Cell Analysis Framework via Conditional Diffusion Generative Models
  ☆30Updated last year
• microsoft / zero-shot-scfoundation
  ☆72Updated last year
• theislab / cpa
  The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell leve…
  ☆112Updated last year
• OmicsML / CellPLM
  Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.
  ☆97Updated last year
• hui2000ji / scETM
  A generative topic model that facilitates integrative analysis of large-scale single-cell RNA sequencing data.
  ☆53Updated 3 years ago
• EperLuo / scDiffusion
  A model developed for the generation of scRNA-seq data
  ☆73Updated 7 months ago
• jsxlei / scCLIP
  ☆30Updated last year
• aaronwtr / PertEval
  Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.
  ☆26Updated 2 months ago
• theislab / CellFlow
  Modeling complex perturbations with CellFlow
  ☆87Updated last week
• mims-harvard / PINNACLE
  Contextual AI models for single-cell protein biology
  ☆88Updated 7 months ago
• const-ae / linear_perturbation_prediction-Paper
  ☆54Updated 2 months ago
• jingcheng-du / Gene2vec
  Gene2Vec: Distributed Representation of Genes Based on Co-Expression
  ☆125Updated 3 years ago
• Genentech / sVAE
  ☆63Updated 2 years ago
• addiewc / Sagittarius
  Gene expression time-series extrapolation for heterogeneous data
  ☆18Updated 2 years ago
• rvinas / HYFA
  Hypergraph Factorisation
  ☆26Updated 10 months ago
• yulun-rayn / graphVCI
  Predicting Cellular Responses with Variational Causal Inference and Refined Relational Information (ICLR 2023)
  ☆19Updated 3 months ago
• bunnech / cellot
  Learning Single-Cell Perturbation Responses using Neural Optimal Transport
  ☆146Updated 11 months ago
• HantaoShu / DeepSEM
  ☆85Updated 2 years ago
• Genentech / iterative-perturb-seq
  Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors
  ☆40Updated last year
• OmicsML / scMoFormer
  Single-Cell Multimodal Prediction via Transformer
  ☆28Updated last year
• HelloWorldLTY / scELMo
  Codes for paper: scELMo: Embeddings from Language Models are Good Learners for Single-cell Data Analysis
  ☆14Updated 9 months ago
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆164Updated 3 years ago
• Genentech / PerturbQA
  ☆23Updated 2 weeks ago
• dohlee / chromoformer
  The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
  ☆36Updated 2 years ago
• snap-stanford / mars
  Discovering novel cell types across heterogenous single-cell experiments
  ☆123Updated 2 years ago
• ruiyi-zhang / scPretrain
  scPretrain: Multi-task self-supervised learning for cell type classification
  ☆23Updated 3 years ago