Python package for graph neural networks in chemistry and biology
- deep-learning
- graph-neural-networks
- dgl
- cheminformatics
Repository Index
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In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
- dna
- k-mer
- python
- bloom-filter
A Go package for engineering organisms.
- synthetic-biology
- synbio
- genetic-engineering
- molecular-biology
Interactive network visualization in Python and Dash, powered by Cytoscape.js
- plotly-dash
- plotly
- dash
- cytoscape
The Chemistry Development Kit
- code4lib
- chemistry
- java
- cheminformatics
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
- sequence-alignment
- edit-distance
- levehnstein-distance
- library
Molecular Processing Made Easy.
- python
- molecule
- rdkit
- drug-discovery
Vision-Language Pathology Foundation Model - Nature Medicine
- bioimage-analysis
- bioimage-informatics
- conch
- foundation-model
Dicoogle - Open Source PACS
- dicoogle
- dicom
- pacs
- medical-imaging
Graph-linked unified embedding for single-cell multi-omics data integration
- bioinformatics
- deep-learning
- single-cell
- single-cell-multiomics
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
Universal cheminformatics toolkit, utilities and database search tools
- indigo
- bingo
- cheminformatics
- chemistry
Deep Reinforcement Learning for de-novo Drug Design
- deeplearning
- reinforcement-learning
- cheminformatics
- molecular-modeling
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
MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)
Graph-based molecule modeling toolkit for cheminformatics
- cheminformatics
- molecular-modeling
- chemistry
- toolkit
Molecule Validation and Standardization
- rdkit
- python
- chemistry
- cheminformatics
AI-based pathology predicts origins for cancers of unknown primary - Nature
- histology
- pathology
- wsi-images
- histopathology
Open source tumor evidence matching for sequencing labs and hospitals without molecular tumor boards. Research prototype; oncologist review required.
- bioinformatics
- cancer-research
- computational-biology
- drug-repurposing
ChemML is a machine learning and informatics program suite for the chemical and materials sciences.
- quantum-mechanics
- materials-informatics
- data-science
- machine-learning
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
Data visualisation web components for the life sciences.
- biohackeu21
- bioinformatics
- visualization
- webcomponents
A tool for cell instance aware segmentation in densely packed 3D volumetric images
- segmentation
- deep-learning
- bioinformatics
- neural-network