JiriBruthans

JiriBruthans's Stars

• theislab/prophet

  Language:Python252

• jkobject/scPRINT

  single cell foundation model for Gene network inference and more

  Language:Jupyter Notebook133

• theislab/single-cell-transformer-papers

  26931

• ur-whitelab/LLMs-in-science

  16520

• snap-stanford/BioDiscoveryAgent

  BioDiscoveryAgent is an LLM-based AI agent for closed-loop design of genetic perturbation experiments

  Language:Python254

• Genentech/gReLU

  gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.

  Language:Python23023

• theislab/scgen

  Single cell perturbation prediction

  Language:Python26956

• evo-design/evo

  Biological foundation modeling from molecular to genome scale

  Language:Jupyter Notebook1.1k135

• KrishnaswamyLab/TrajectoryNet

  TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics

  Language:Jupyter Notebook10014

• single-cell-data/TileDB-SOMA

  Python and R SOMA APIs using TileDB’s cloud-native format. Ideal for single-cell data at any scale.

  Language:Python9325

• chanzuckerberg/cellxgene

  An interactive explorer for single-cell transcriptomics data

  Language:JavaScript636119

• czbiohub-sf/cellxgene

  An interactive explorer for single-cell transcriptomics data

  Language:Python61

• theislab/single-cell-best-practices

  https://www.sc-best-practices.org

  Language:Jupyter Notebook785190

• Opentrons/opentrons

  Software for writing protocols and running them on the Opentrons Flex and Opentrons OT-2

  Language:Python429179

• snap-stanford/UCE

  UCE is a zero-shot foundation model for single-cell gene expression data

  Language:Python16429

• scverse/scvi-tools

  Deep probabilistic analysis of single-cell and spatial omics data

  Language:Python1.3k356

• facebookresearch/esm

  Evolutionary Scale Modeling (esm): Pretrained language models for proteins

  Language:Python3.3k643

• snap-stanford/SATURN

  Language:Jupyter Notebook10817

• yiqunchen/GenePT

  Language:Jupyter Notebook17827

• jingcheng-du/Gene2vec

  Gene2Vec: Distributed Representation of Genes Based on Co-Expression

  Language:Python10827

• aristoteleo/dynamo-release

  Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses

  Language:Python42459

• JBEI/ART

  A machine learning tool to improve the effectiveness of strain engineering in synthetic biology

  Language:Jupyter Notebook5420

• CIDARLAB/cello

  Genetic circuit design automation

  Language:Java810137

• bowang-lab/scGPT

  Language:Jupyter Notebook1.1k207

• asncd/MIMOSCA

  A repository for the design and analysis of pooled single cell RNA-seq perturbation experiments.

  Language:Jupyter Notebook8725

• Luthey-Schulten-Lab/Lattice_Microbes

  Language:HTML325

• jerryji1993/DNABERT

  DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

  Language:Python604158

• dauparas/ProteinMPNN

  Code for the ProteinMPNN paper

  Language:Jupyter Notebook1.1k307

• Significant-Gravitas/Auto-GPT-Plugins

  Plugins for Auto-GPT

  Language:Python3.9k563

• Significant-Gravitas/AutoGPT

  AutoGPT is the vision of accessible AI for everyone, to use and to build on. Our mission is to provide the tools, so that you can focus on what matters.

  Language:Python169k44.5k