Repository Index

Generation of protein sequences and evolutionary alignments via discrete diffusion models

• discrete-diffusion
• generative-model
• multiple-sequence-alignment
• protein-sequences

Fast, sensitive and accurate integration of single-cell data with Harmony

• scrna-seq
• algorithm
• data-integration
• r

Graph-linked unified embedding for single-cell multi-omics data integration

• bioinformatics
• deep-learning
• single-cell
• single-cell-multiomics

Benchmarking analysis of data integration tools

Reference mapping for single-cell genomics

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

Schema and generated objects for biolink data model and upper ontology

• biolink
• monarchinitiative
• gene-ontology
• datamodel

A Network Integration Approach for Drug-Target Interaction Prediction

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

• ai4science
• llm
• multiagent-systems
• prompt-engineering

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

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

PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).

• deep-generative-model
• deep-learning
• single-cell-data-integration
• single-cell-multiomics

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

Multigrate: multiomic data integration for single-cell genomics

Official implementation of JAMIE, Joint variational Autoencoders for Multimodal Imputation and Embedding

• autoencoder
• imputation
• integration
• multimodal

Analysis of cell migration in Igor Pro

• igor
• imagej
• cell-migration
• tracking