Alternatives and similar repositories for iterative-perturb-seq

Users that are interested in iterative-perturb-seq are comparing it to the libraries listed below

• mims-harvard / PDGrapher
  Combinatorial prediction of therapeutic perturbations using causally-inspired neural networks
  ☆28Updated 3 months ago
• johli / scrambler
  Interpretation by Deep Generative Masking for Biological Sequences
  ☆37Updated 3 years ago
• bowang-lab / BIONIC
  Biological Network Integration using Convolutions
  ☆62Updated last year
• theislab / chemCPA
  Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
  ☆122Updated 6 months ago
• microsoft / zero-shot-scfoundation
  ☆72Updated last year
• aaronwtr / PertEval
  Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.
  ☆27Updated 3 weeks ago
• bowang-lab / scFormer
  ☆19Updated 2 years 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
• bowang-lab / Orthrus
  Orthrus is a mature RNA model for RNA property prediction. It uses a mamba encoder backbone, a variant of state-space models specifical…
  ☆74Updated 2 weeks ago
• dohlee / chromoformer
  The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
  ☆36Updated 2 years ago
• theislab / cpa
  The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell leve…
  ☆109Updated last year
• oxpig / saab_plus
  ☆25Updated 5 years ago
• TuftsBCB / RegDiffusion
  Diffusion model for gene regulatory network inference.
  ☆23Updated last month
• evanseitz / squid-nn
  surrogate quantitative interpretability for deepnets
  ☆24Updated 2 weeks ago
• snap-stanford / KGWAS
  KGWAS: novel genetics discovery enabled by massive functional genomics knowledge graph
  ☆73Updated 5 months ago
• KatarinaYuan / awesome-single-cell-foundation
  Paper collection for single cell foundation models
  ☆32Updated last year
• mims-harvard / PINNACLE
  Contextual AI models for single-cell protein biology
  ☆88Updated 6 months ago
• epigen / KPNN
  Knowledge-primed neural networks
  ☆38Updated 2 years ago
• hui2000ji / scETM
  A generative topic model that facilitates integrative analysis of large-scale single-cell RNA sequencing data.
  ☆52Updated 3 years ago
• frederikkemarin / BEND
  Benchmarking DNA Language Models on Biologically Meaningful Tasks
  ☆122Updated 9 months ago
• OATML / EVE
  Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…
  ☆67Updated 2 years ago
• jmschrei / ledidi
  Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.
  ☆87Updated 2 months ago
• carpenter-singh-lab / 2022_Haghighi_NatureMethods
  High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
  ☆50Updated 2 weeks ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆60Updated 4 months ago
• krishnanlab / obnb
  A Python toolkit for setting up benchmarking dataset using biomedical networks
  ☆22Updated last week
• Sanofi-Public / CodonBERT
  Repository for mRNA Paper and CodonBERT publication.
  ☆133Updated last year
• lucidrains / tf-bind-transformer
  A repository with exploration into using transformers to predict DNA ↔ transcription factor binding
  ☆85Updated 3 years ago
• const-ae / linear_perturbation_prediction-Paper
  ☆47Updated last month
• AstraZeneca / skywalkR
  code for Gogleva et al manuscript
  ☆45Updated 2 years ago
• Genentech / sVAE
  ☆63Updated 2 years ago