Alternatives and similar repositories for scFoundation:

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

• theislab / single-cell-transformer-papers
  ☆310Updated 2 months ago
• snap-stanford / GEARS
  GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
  ☆251Updated 3 months ago
• OmicsML / awesome-foundation-model-single-cell-papers
  ☆273Updated 2 weeks ago
• TencentAILabHealthcare / scBERT
  ☆307Updated last year
• snap-stanford / UCE
  UCE is a zero-shot foundation model for single-cell gene expression data
  ☆189Updated 2 months ago
• jkobject / geneformer
  ☆64Updated last year
• yiqunchen / GenePT
  ☆258Updated last year
• ArcInstitute / arc-virtual-cell-atlas
  Arc Virtual Cell Atlas
  ☆273Updated last week
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆185Updated 2 months ago
• xCompass-AI / GeneCompass
  GeneCompass
  ☆77Updated 9 months ago
• PharMolix / LangCell
  Code for "LangCell: Language-Cell Pre-training for Cell Identity Understanding".
  ☆58Updated 4 months ago
• gao-lab / GLUE
  Graph-linked unified embedding for single-cell multi-omics data integration
  ☆407Updated last month
• JackieHanLab / TOSICA
  Transformer for One-Stop Interpretable Cell-type Annotation
  ☆139Updated last year
• vandijklab / cell2sentence
  Cell2Sentence: Teaching Large Language Models the Language of Biology
  ☆130Updated 2 weeks ago
• HelloWorldLTY / scEval
  Codes for paper: Evaluating the Utilities of Large Language Models in Single-cell Data Analysis.
  ☆69Updated 3 months ago
• Winnie09 / GPTCelltype
  ☆195Updated last year
• theislab / nicheformer
  Repository for Nicheformer: a foundation model for single-cell and spatial omics
  ☆90Updated last month
• apeterswu / Awesome-Bio-Foundation-Models
  A collection of awesome bio-foundation models, including protein, RNA, DNA, gene, single-cell, and so on.
  ☆218Updated last week
• OmicsML / awesome-deep-learning-single-cell-papers
  ☆762Updated 2 weeks ago
• morris-lab / CellOracle
  This is the alpha version of the CellOracle package
  ☆348Updated 3 months ago
• theislab / chemCPA
  Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
  ☆112Updated 3 months ago
• theislab / scib
  Benchmarking analysis of data integration tools
  ☆348Updated 3 months ago
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆124Updated 2 months ago
• ml4bio / RNA-FM
  Nature Methods: RNA foundation model (together with RhoFold)
  ☆267Updated last week
• SuperBianC / scMulan
  Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
  ☆57Updated 11 months ago
• OmicsML / CellPLM
  Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.
  ☆84Updated last year
• xianglin226 / Benchmarking-Single-Cell-Perturbation
  Single-Cell (Perturbation) Model Library
  ☆55Updated last month
• Teichlab / celltypist
  A tool for semi-automatic cell type classification
  ☆359Updated last week
• Genentech / gReLU
  gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
  ☆260Updated 3 weeks ago
• snap-stanford / SATURN
  ☆124Updated 10 months ago