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.
Repository Index
47,133 repositories indexed
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:christmas_tree:Visualization and annotation of phylogenetic trees
- r
- visualization
- phylogenetic-trees
- annotations
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
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
- sequence-alignment
- edit-distance
- levehnstein-distance
- library
Spatial Single Cell Analysis in Python
- single-cell-rna-seq
- single-cell-genomics
- spatial-transcriptomics
- spatial-analysis
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
Data visualisation web components for the life sciences.
- biohackeu21
- bioinformatics
- visualization
- webcomponents
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
Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders
- epigenomics
- pattern-search
- data-visualization
- interactive-machine-learning
Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
- foundation-models
- gpt
- single-cell
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning
Deciphering cell-cell communication from spatially resolved transcriptomic data at single-cell resolution with subgraph-based attentional graph neural network
Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.
- postgres
- postgresql
- python
- infectious-disease
DetecDiv provides a comprehensive set of tools to analyze time microscopy images using deep learning methods. The software structure is such that data can be processed either at the command line or using a graphical user-interface. Detecdiv classification models include : image classification and regression, semantic segmentation, LSTM networks to analyze data and image timeseries.