Repository Index

code to run sei and obtain sei and sequence class predictions

Structural variant detection and association testing

Rails frontend to The Genome Institute's drug gene interaction database.

PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.

Toolbox for the analysis of smFISH images.

• pattern-classification
• rna-localization
• segmentation
• smfish

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

• computational-biology
• bioinformatics
• graph-convolution
• deep-learning

Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders

• epigenomics
• pattern-search
• data-visualization
• interactive-machine-learning

The framework for quantification of neuronal anatomy

• neuroscience
• neuroanatomy-toolbox
• imagej
• imagej2

Tool for precise, interactive, fast and scalable FISH spot detection

Predicting Cell Health with Morphological Profiles

• carpenter-lab
• morphological-profiling
• crispr
• cell-painting

PyTorch implementation of "TGSA: Protein-Protein Association-Based Twin Graph Neural Networks for Drug Response Prediction with Similarity Augmentation"

Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.

• postgres
• postgresql
• python
• infectious-disease

scPair: Boosting single cell multimodal analysis by leveraging single cell atlases and implicit feature selection

DeepAEG: A model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies

Interpretable drug response prediction with graph neural networks over drugs, cell lines, and genes.

GNN-based gene-selection deep learning model for drug response prediction