Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
- drug-discovery
- quantum-chemistry
- deep-learning
- biology
Repository Index
47,133 repositories indexed
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The repository host gives no description.
Deep probabilistic analysis of single-cell and spatial omics data
- scrna-seq
- variational-bayes
- variational-autoencoder
- cite-seq
Biological foundation modeling from molecular to genome scale
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
Cloud-native genomic dataframes and batch computing
- genetics
- vcf
- genomics
- gwas
:christmas_tree:Visualization and annotation of phylogenetic trees
- r
- visualization
- phylogenetic-trees
- annotations
Python package for graph neural networks in chemistry and biology
- deep-learning
- graph-neural-networks
- dgl
- cheminformatics
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
- foundation-models
- genomics
- language-models
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
- kmer
- dnabert-model
- kmer-format
- gpu
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
A Go package for engineering organisms.
- synthetic-biology
- synbio
- genetic-engineering
- molecular-biology
Official release of the ProGen models
- language-model
- protein
- generative-model
Generation of protein sequences and evolutionary alignments via discrete diffusion models
- discrete-diffusion
- generative-model
- multiple-sequence-alignment
- protein-sequences
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
- variant-calling
- genomics
- vcf-manipulation
- genotyping
Generative biopolymer design with rich conditioning.
[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
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
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
The repository host gives no description.
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