Generation of protein sequences and evolutionary alignments via discrete diffusion models
- discrete-diffusion
- generative-model
- multiple-sequence-alignment
- protein-sequences
Repository Index
47,133 repositories indexed
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[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
Graph-linked unified embedding for single-cell multi-omics data integration
- bioinformatics
- deep-learning
- single-cell
- single-cell-multiomics
Multi-Omics Factor Analysis
- multi-omics
- factor-analysis
- mofa
GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
Reference mapping for single-cell genomics
- single-cell
- deep-learning
- rna-seq-analysis
- data-integration
Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell
- histology
- wsi-images
- pan-cancer-analysis
- genomics
Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
- cancer-genomics
- cnv-detection
- single-cell
- phylogeny
MOGONET (Multi-Omics Graph cOnvolutional NETworks) is a novel multi-omics data integrative analysis framework for classification tasks in biomedical applications.
Integrated pipeline for multiplexed image analysis
- multiplexed-imaging
- python
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
- ai4science
- llm
- multiagent-systems
- prompt-engineering
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
Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
- cell-annotation
- multiplexed-imaging
- mpif
Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
- foundation-models
- gpt
- single-cell
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
- single-cell
- scrna-seq
- scatac-seq
- deep-neural-networks
Multigrate: multiomic data integration for single-cell genomics
Official implementation of JAMIE, Joint variational Autoencoders for Multimodal Imputation and Embedding
- autoencoder
- imputation
- integration
- multimodal
scPair: Boosting single cell multimodal analysis by leveraging single cell atlases and implicit feature selection