Repository Index

Foundation Models for Genomics & Transcriptomics

• genomics
• deep-learning
• transformer
• dna

Reference mapping for single-cell genomics

• single-cell
• deep-learning
• rna-seq-analysis
• data-integration

Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star

• dna
• language-model
• variant-effect-prediction
• genomics

The repository host gives no description.

Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

• histology
• wsi-images
• pan-cancer-analysis
• genomics

🏃 The go-to single-cell Foundation Model

• batch-correction
• cell-biology
• celltype-annotation
• denoising

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

• disentanglement
• drug-discovery
• genomics
• perturbation

GeneCompass

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

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

Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.

• foundation-models
• gpt
• single-cell

High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations

The repository host gives no description.

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