Official git repository for Biopython (originally converted from CVS)
- python
- bioinformatics
- genomics
- biopython
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DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
- tensorflow
- deep-neural-network
- genomics
- science
Making Protein folding accessible to all!
- bioinformatics
- multiple-sequence-alignment
- protein-structure
- structure-prediction
Single-cell analysis in Python. Scales to >100M cells.
- machine-learning
- data-science
- visualize-data
- transcriptomics
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
- fastq
- qc
- preprocessing
- filtering
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
Official code repository for GATK versions 4 and up
Data intensive science for everyone.
This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
- bioinformatics
- sequence-alignment
- genomics
- fm-index
Open source tools for computational pathology - Nature BME
- histopathology
- pathology
- weakly-supervised-learning
- whole-slide-imaging
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
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.
C library for high-throughput sequencing data formats
- htslib
- bioinformatics
- sam
- bam
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
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