Chai-1, SOTA model for biomolecular structure prediction
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ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
- drug-repurposing
- deep-learning
- drug-target-interactions
- toolkit
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Foundation Models for Genomics & Transcriptomics
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
- dna
- k-mer
- python
- bloom-filter
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
- kmer
- dnabert-model
- kmer-format
- gpu
A Go package for engineering organisms.
- synthetic-biology
- synbio
- genetic-engineering
- molecular-biology
Spatial Single Cell Analysis in Python
- single-cell-rna-seq
- single-cell-genomics
- spatial-transcriptomics
- spatial-analysis
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
- bioinformatics
- taxonomy
- cross-platform
- lineage
Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk
- bioinformatics
- exact-optimization
- metabolomics
- paired-data
Genomic sequence storage, indexing and alignment inside PostgreSQL: https://bioseqdb.com/
- alignment
- bioinformatics
- biology
- database
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
LLM for Drug Editing, ICLR 2024
- chatgpt
- conversation
- drug
- drug-discovery
TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524
- self-attention
- compound-protein-interaction
- transformercpi
- structure-free-virtual-sreening
Learning cell communication from spatial graphs of cells
- tensorflow
- gnn
- glm
- cvae
Rails frontend to The Genome Institute's drug gene interaction database.
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
Adaptive Graph Attention Auto-encoder for Spatial Domain Identification of Spatial Transcriptomics
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning
Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.
- postgres
- postgresql
- python
- infectious-disease
DetecDiv provides a comprehensive set of tools to analyze time microscopy images using deep learning methods. The software structure is such that data can be processed either at the command line or using a graphical user-interface. Detecdiv classification models include : image classification and regression, semantic segmentation, LSTM networks to analyze data and image timeseries.