ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
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Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
- foundation-models
- genomics
- language-models
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
- variant-calling
- genomics
- vcf-manipulation
- genotyping
Fast, sensitive and accurate integration of single-cell data with Harmony
Generative biopolymer design with rich conditioning.
Sequential regulatory activity predictions with deep convolutional neural networks.
RNA-seq prediction with deep convolutional neural networks.
talk with NCBI entrez using R
PhyloNetworks: a julia package with utilities for phylogenetic networks
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
Interpretable bilinear attention network with domain adaptation improves drug-target prediction.
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
Predicting Cell Health with Morphological Profiles
- carpenter-lab
- morphological-profiling
- crispr
- cell-painting
Deciphering cell-cell communication from spatially resolved transcriptomic data at single-cell resolution with subgraph-based attentional graph neural network
PyTorch implementation of "TGSA: Protein-Protein Association-Based Twin Graph Neural Networks for Drug Response Prediction with Similarity Augmentation"