Alternatives and similar repositories for nicheformer

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

• OmicsML / CellPLM
  Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.
  ☆99Updated last year
• EperLuo / scDiffusion
  A model developed for the generation of scRNA-seq data
  ☆78Updated 8 months ago
• snap-stanford / UCE
  UCE is a zero-shot foundation model for single-cell gene expression data
  ☆224Updated 8 months ago
• bowang-lab / scGPT-spatial
  ☆113Updated 9 months ago
• YangLabHKUST / SpatialScope
  A unified approach for integrating spatial and single-cell transcriptomics data by leveraging deep generative models
  ☆73Updated last year
• siyuh / Squidiff
  ☆42Updated last week
• xianglin226 / Benchmarking-Single-Cell-Perturbation
  Single-Cell (Perturbation) Model Library
  ☆81Updated 2 months ago
• cantinilab / scPRINT
  🏃 The go-to single-cell Foundation Model
  ☆117Updated last week
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆151Updated 8 months ago
• nitzanlab / biolord
  ☆86Updated last year
• clinicalml / sc-foundation-eval
  Code for evaluating single cell foundation models scBERT and scGPT
  ☆46Updated last year
• theislab / CellFlow
  Modeling complex perturbations with CellFlow
  ☆95Updated last week
• const-ae / linear_perturbation_prediction-Paper
  ☆58Updated 3 months ago
• SuperBianC / scMulan
  Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
  ☆59Updated last year
• JackieHanLab / TOSICA
  Transformer for One-Stop Interpretable Cell-type Annotation
  ☆144Updated last year
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆167Updated 3 years ago
• kpcoleman / miso
  ☆31Updated 9 months ago
• snap-stanford / SATURN
  ☆143Updated last year
• ZJUFanLab / scCube
  an SRT simulator for simulating multiple spatial variability in spatial resolved transcriptomics and generating unbiased simulated SRT da…
  ☆25Updated 8 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.
  ☆63Updated last week
• jkobject / geneformer
  ☆84Updated 2 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
  ☆53Updated 4 months ago
• theislab / cpa
  The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell leve…
  ☆118Updated last year
• biomed-AI / CellFM
  ☆85Updated 2 months ago
• ludvb / xfuse
  Super-resolved spatial transcriptomics by deep data fusion
  ☆74Updated 2 years ago
• xCompass-AI / GeneCompass
  GeneCompass
  ☆98Updated last month
• JinmiaoChenLab / GraphST
  ☆138Updated last year
• theislab / prophet
  ☆37Updated last week
• Lotfollahi-lab / nichecompass
  End-to-end analysis of spatial multi-omics data
  ☆95Updated last week
• bunnech / cellot
  Learning Single-Cell Perturbation Responses using Neural Optimal Transport
  ☆150Updated last year