Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
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ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Precision Medicine Knowledge Graph (PrimeKG)
- knowledge-graph
- precision-medicine
- therapeutics
- bioinformatics
Python package for graph neural networks in chemistry and biology
- deep-learning
- graph-neural-networks
- dgl
- cheminformatics
Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
- deep-learning
- protein-sequences
- protein-structure
- semi-supervised-learning
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
Official repository for the ProteinGym benchmarks
- benchmark
- computational-biology
- protein
- protein-design
Sequential regulatory activity predictions with deep convolutional neural networks.
Benchmarking analysis of data integration tools
Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star
- dna
- language-model
- variant-effect-prediction
- genomics
RNA-seq prediction with deep convolutional neural networks.
A Network Integration Approach for Drug-Target Interaction Prediction
MOGONET (Multi-Omics Graph cOnvolutional NETworks) is a novel multi-omics data integrative analysis framework for classification tasks in biomedical applications.
PhyloNetworks: a julia package with utilities for phylogenetic networks
OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.
🏃 The go-to single-cell Foundation Model
- batch-correction
- cell-biology
- celltype-annotation
- denoising
Interpretable bilinear attention network with domain adaptation improves drug-target prediction.
A tool for cell instance aware segmentation in densely packed 3D volumetric images
- segmentation
- deep-learning
- bioinformatics
- neural-network
code to run sei and obtain sei and sequence class predictions
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
NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
- computational-biology
- bioinformatics
- graph-convolution
- deep-learning
The framework for quantification of neuronal anatomy
- neuroscience
- neuroanatomy-toolbox
- imagej
- imagej2