Alternatives and similar repositories for PINNACLE

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

• theislab / chemCPA
  Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
  ☆123Updated 6 months ago
• dohlee / chromoformer
  The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
  ☆36Updated 2 years ago
• Perturbation-Response-Prediction / PRnet
  PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturb…
  ☆57Updated 8 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
  ☆44Updated last month
• myzhengSIMM / TranSiGen
  ☆31Updated 7 months ago
• jkobject / geneformer
  ☆76Updated 2 weeks ago
• snap-stanford / KGWAS
  KGWAS: novel genetics discovery enabled by massive functional genomics knowledge graph
  ☆73Updated 5 months ago
• wukevin / tcr-bert
  Large language modeling applied to T-cell receptor (TCR) sequences.
  ☆56Updated 3 years ago
• idekerlab / DrugCell
  A visible neural network model for drug response prediction
  ☆148Updated last year
• microsoft / zero-shot-scfoundation
  ☆72Updated last year
• Sanofi-Public / CodonBERT
  Repository for mRNA Paper and CodonBERT publication.
  ☆134Updated last year
• snap-stanford / GEARS
  GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
  ☆288Updated 7 months ago
• hosseinshn / MOLI
  MOLI: Multi-Omics Late Integration with deep neural networks for drug response prediction
  ☆55Updated 4 years ago
• ArcInstitute / state
  State is a machine learning model that predicts cellular perturbation response across diverse contexts
  ☆355Updated this week
• KangBoming / BulkFormer
  BulkFormer: A large-scale foundation model for human bulk transcriptomes
  ☆19Updated last month
• genbio-ai / ModelGenerator
  AIDO.ModelGenerator is a software stack powering the development of an AI-driven Digital Organism (AIDO) by enabling researchers to adapt…
  ☆93Updated this week
• aaronwtr / PertEval
  Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.
  ☆27Updated last month
• Genentech / SpatialAgent
  ☆124Updated 4 months ago
• Genentech / iterative-perturb-seq
  Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors
  ☆40Updated last year
• KatarinaYuan / awesome-single-cell-foundation
  Paper collection for single cell foundation models
  ☆32Updated last year
• jump-cellpainting / datasets
  Images and other data from the JUMP Cell Painting Consortium
  ☆174Updated last week
• yhr91 / GEARS_misc
  ☆20Updated 10 months ago
• TencentAILabHealthcare / DeepAIR
  ☆37Updated 2 years ago
• phbradley / TCRdock
  python tools for TCR:peptide-MHC modeling and analysis
  ☆81Updated last year
• bowang-lab / genomic-FM
  ☆29Updated last week
• HelloWorldLTY / scEval
  Codes for paper: Evaluating the Utilities of Large Language Models in Single-cell Data Analysis.
  ☆72Updated 2 months ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆60Updated 5 months ago
• chenkenbio / SpliceBERT
  Primary RNA sequence model
  ☆38Updated last year
• jianglikun / DeepTTC
  DeepTTC: a transformer-based model for predicting cancer drug response
  ☆16Updated 2 years ago
• bsml320 / VAEN
  A deep generative neural network based approach to impute drug response
  ☆21Updated 4 years ago