Repository Index

Official git repository for Biopython (originally converted from CVS)

• python
• bioinformatics
• genomics
• biopython

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.

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

• drug-repurposing
• deep-learning
• drug-target-interactions
• toolkit

🦖 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

• workflow-execution
• workflow
• cloud
• hpc

Cloud-native genomic dataframes and batch computing

• genetics
• vcf
• genomics
• gwas

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

• spark
• big-data
• bioinformatics
• genomics

C library for high-throughput sequencing data formats

• htslib
• bioinformatics
• sam
• bam

Foundation Models for Genomics & Transcriptomics

• genomics
• deep-learning
• transformer
• dna

Precision Medicine Knowledge Graph (PrimeKG)

• knowledge-graph
• precision-medicine
• therapeutics
• bioinformatics

Python package for graph neural networks in chemistry and biology

• deep-learning
• graph-neural-networks
• dgl
• cheminformatics

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

• dna
• k-mer
• python
• bloom-filter

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

• kmer
• dnabert-model
• kmer-format
• gpu

A Go package for engineering organisms.

• synthetic-biology
• synbio
• genetic-engineering
• molecular-biology

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

• sequence-alignment
• edit-distance
• levehnstein-distance
• library

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

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)

Genomic sequence storage, indexing and alignment inside PostgreSQL: https://bioseqdb.com/

• alignment
• bioinformatics
• biology
• database

Repository for Nicheformer: a foundation model for single-cell and spatial omics

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