Official git repository for Biopython (originally converted from CVS)
- python
- bioinformatics
- genomics
- biopython
Repository Index
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Biomni: a general-purpose biomedical AI agent
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
- pytorch
- protein-structure
- alphafold2
Making Protein folding accessible to all!
- bioinformatics
- multiple-sequence-alignment
- protein-structure
- structure-prediction
NeuroKit2: The Python Toolbox for Neurophysiological Signal Processing
- python
- ecg
- eda
- emg
A versatile pairwise aligner for genomic and spliced nucleotide sequences
- bioinformatics
- sequence-alignment
- spliced-alignment
- genomics
MMseqs2: ultra fast and sensitive search and clustering suite
- bioinformatics
- sequence-clustering
- profile-search
- sequence-search
🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free.
- ai-agents
- bioinformatics
- equity
- genomics
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
- foundation-models
- genomics
- language-models
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
- kmer
- dnabert-model
- kmer-format
- gpu
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
Generation of protein sequences and evolutionary alignments via discrete diffusion models
- discrete-diffusion
- generative-model
- multiple-sequence-alignment
- protein-sequences
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
- sequence-alignment
- edit-distance
- levehnstein-distance
- library
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
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
Sequential regulatory activity predictions with deep convolutional neural networks.
The repository host gives no description.
talk with NCBI entrez using R
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
Probabilistic cell segmentation for in situ spatial transcriptomics
Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
- disentanglement
- drug-discovery
- genomics
- perturbation
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