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
Biological foundation modeling from molecular to genome scale
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
Official repository for the ProteinGym benchmarks
- benchmark
- computational-biology
- protein
- protein-design
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star
- dna
- language-model
- variant-effect-prediction
- genomics
Schema and generated objects for biolink data model and upper ontology
- biolink
- monarchinitiative
- gene-ontology
- datamodel
Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell
- histology
- wsi-images
- pan-cancer-analysis
- genomics
Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome
- cancer-genomics
- cnv-detection
- single-cell
- phylogeny
Genomic sequence storage, indexing and alignment inside PostgreSQL: https://bioseqdb.com/
- alignment
- bioinformatics
- biology
- database
PhyloNetworks: a julia package with utilities for phylogenetic networks
🏃 The go-to single-cell Foundation Model
- batch-correction
- cell-biology
- celltype-annotation
- denoising
Python package for image-based profiling
- cytominer
- microscopy
- morphological-profiling
- python
NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
- computational-biology
- bioinformatics
- graph-convolution
- deep-learning
NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
- r
- neuroanatomy-toolbox
- cran
- neuron
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
Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
- cell-annotation
- multiplexed-imaging
- mpif
Run scripts, explore your genome, and get personalized explanations — all in natural dialogue.
- analysis
- claude
- claudecode
- dna
High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations