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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Official git repository for Biopython (originally converted from CVS)
- python
- bioinformatics
- genomics
- biopython
Official repository for the Boltz biomolecular interaction models
- binding-prediction
- drug-discovery
- protein-structure
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
- pytorch
- protein-structure
- alphafold2
RNA-seq aligner
Chai-1, SOTA model for biomolecular structure prediction
Deep probabilistic analysis of single-cell and spatial omics data
- scrna-seq
- variational-bayes
- variational-autoencoder
- cite-seq
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.
🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
Foundation Models for Genomics & Transcriptomics
: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
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
Fast, sensitive and accurate integration of single-cell data with Harmony
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
- sequence-alignment
- edit-distance
- levehnstein-distance
- library
A tool for semi-automatic cell type classification
- python
- single-cell
- machine-learning
- scrna-seq
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
GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star
- dna
- language-model
- variant-effect-prediction
- genomics
UCE is a zero-shot foundation model for single-cell gene expression data
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