Graph-linked unified embedding for single-cell multi-omics data integration
- bioinformatics
- deep-learning
- single-cell
- single-cell-multiomics
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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 curated list of resources relevant to doing Biomedical Information Extraction (including BioNLP)
- awesome
- biomedical
- text-mining
- information-extraction
A dependency-free cross-platform swiss army knife for PDB files.
- python
- protein
- pdb
- bioinformatics
Curated (meta)list of resources for Biology.
This repository contains a subset of pointers to solutions with editorials and notes to my trainees (ACM ICPC, OJs, IOI, POI, CEOI, JOI, etc). For IOI/OI, I organized what I found on the web from official solutions and materials.
Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.
- hubmap
- imaging
- openmicroscopy
- ome-tiff
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)
A curated list of resources for machine learning for small-molecule drug discovery
- awesome-list
- machine-learning
- cheminformatics
- drug-discovery
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
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
Apache cTAKES is a Natural Language Processing (NLP) platform for clinical text.
- clinical
- nlp
- bioinformatics
- ai
A tool for cell instance aware segmentation in densely packed 3D volumetric images
- segmentation
- deep-learning
- bioinformatics
- neural-network
OCaml Bioinformatics Library
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
- ai4science
- llm
- multiagent-systems
- prompt-engineering
We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.
- ai-aided-drug-discovery
- awesome
- drug-discovery
- molecular-docking
TypeDB Bio: Biomedical Knowledge Graph
- bioinformatics
- knowledge-graph
- knowledge-base
- drug-discovery
Autonomous multi-agent framework to optimize scientific software
- acceleration
- agentic-ai
- ai-agents
- bioinformatics
NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
- computational-biology
- bioinformatics
- graph-convolution
- deep-learning
:art: Image processing toolbox for R
- r
- bioinformatics
- image-processing
- image-analysis
A library to build and execute typed scientific workflows