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The Top 23 Graph Bioinformatics Open Source Projects

Open source projects categorized as Graph Bioinformatics
Categories > Data Processing > Bioinformatics
Graphein ⭐ 932
Protein Graph Library
dependent packages 1total releases 29most recent commit 4 months agopypi graphein} Downloads
Dgl Lifesci ⭐ 558
Python package for graph neural networks in chemistry and biology
dependent packages 4total releases 17most recent commit a year agopypi dgllife} Downloads
Grakel ⭐ 540
A scikit-learn compatible library for graph kernels
dependent packages 1total releases 5most recent commit 6 months agopypi grakel-dev} Downloads
Hifiasm ⭐ 443
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
most recent commit 3 months ago
React Cytoscapejs ⭐ 407
React component for Cytoscape.js network visualisations
dependent packages 34total releases 7most recent commit a year agonpm react-cytoscapejs} Downloads
Minigraph ⭐ 367
Proof-of-concept seq-to-graph mapper and graph generator
total releases 1most recent commit 4 months ago
Canvasxpress ⭐ 282
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
dependent packages 4total releases 43most recent commit 3 months ago
Ppanggolin ⭐ 191
Build a partitioned pangenome graph from microbial genomes
total releases 6most recent commit 3 months ago
Gfatools ⭐ 181
Tools for manipulating sequence graphs in the GFA and rGFA formats
most recent commit 6 months ago
Graphtyper ⭐ 156
Population-scale genotyping using pangenome graphs
most recent commit 3 months ago
Ontobio ⭐ 114
python library for working with ontologies and ontology associations
dependent packages 2total releases 190most recent commit 3 months agopypi ontobio} Downloads
Bio4j ⭐ 112
Bio4j abstract model and general entry point to the project
most recent commit 7 years ago
Spacegraphcats ⭐ 112
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
total releases 15most recent commit 3 months ago
Tutorial ⭐ 94
Tutorials on machine learning, artificial intelligence, data science with math explanation and reusable code (in python and R)
most recent commit 3 months ago
Bcalm ⭐ 90
compacted de Bruijn graph construction in low memory
most recent commit a year ago
Pybel ⭐ 89
🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)
dependent packages 52total releases 91most recent commit 2 years agopypi pybel} Downloads
Arcs ⭐ 86
🌈Scaffold genome sequence assemblies using linked or long read sequencing data
most recent commit 4 months ago
Pygr ⭐ 84
Python graph database framework for bioinformatics
most recent commit 9 years ago
Fermi Lite ⭐ 67
Standalone C library for assembling Illumina short reads in small regions
most recent commit a year ago
Gatb Core ⭐ 61
Core library of the Genome Analysis Toolbox with de-Bruijn graph
most recent commit 5 months ago
Nxontology ⭐ 59
NetworkX-based Python library for representing ontologies
dependent packages 2total releases 15most recent commit 9 months agopypi nxontology} Downloads
Gbwt ⭐ 55
Substring index for paths in a graph
most recent commit 5 months ago
Graph Network Explainability ⭐ 51
Explainability techniques for Graph Networks, applied to a synthetic dataset and an organic chemistry task. Code for the workshop paper "Explainability Techniques for Graph Convolutional Networks" (ICML19)
most recent commit 4 years ago
The 10 Most Depended On Graph Bioinformatics Open Source Projects
Pybel ⭐ 89
🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)
dependent packages 52total releases 91latest release February 11, 2022most recent commit 2 years agopypi pybel} Downloads
React Cytoscapejs ⭐ 407
React component for Cytoscape.js network visualisations
dependent packages 34total releases 7latest release September 02, 2022most recent commit a year agonpm react-cytoscapejs} Downloads
Dgl Lifesci ⭐ 558
Python package for graph neural networks in chemistry and biology
dependent packages 4total releases 17latest release December 21, 2022most recent commit a year agopypi dgllife} Downloads
Canvasxpress ⭐ 282
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
dependent packages 4total releases 43latest release November 08, 2023most recent commit 3 months ago
Algebra ⭐ 10
A Boolean Algebra for Genetic Variants
dependent packages 2total releases 18latest release December 04, 2023most recent commit 3 months agopypi mutalyzer-algebra} Downloads
Ontobio ⭐ 114
python library for working with ontologies and ontology associations
dependent packages 2total releases 190latest release December 01, 2023most recent commit 3 months agopypi ontobio} Downloads
Nxontology ⭐ 59
NetworkX-based Python library for representing ontologies
dependent packages 2total releases 15latest release February 28, 2023most recent commit 9 months agopypi nxontology} Downloads
Grakel ⭐ 540
A scikit-learn compatible library for graph kernels
dependent packages 1total releases 5latest release September 09, 2019most recent commit 6 months agopypi grakel-dev} Downloads
Gfapy ⭐ 39
Gfapy: a flexible and extensible software library for handling sequence graphs in Python
dependent packages 1total releases 16latest release February 03, 2022most recent commit 2 years agopypi gfapy} Downloads
Graphein ⭐ 932
Protein Graph Library
dependent packages 1total releases 29latest release October 27, 2023most recent commit 4 months agopypi graphein} Downloads
The 10 Latest Releases In Graph Bioinformatics Open Source Projects
Algebra ⭐ 10
A Boolean Algebra for Genetic Variants
dependent packages 2total releases 18latest release December 04, 2023most recent commit 3 months agopypi mutalyzer-algebra} Downloads
Ontobio ⭐ 114
python library for working with ontologies and ontology associations
dependent packages 2total releases 190latest release December 01, 2023most recent commit 3 months agopypi ontobio} Downloads
Canvasxpress ⭐ 282
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
dependent packages 4total releases 43latest release November 08, 2023most recent commit 3 months ago
Graphein ⭐ 932
Protein Graph Library
dependent packages 1total releases 29latest release October 27, 2023most recent commit 4 months agopypi graphein} Downloads
Minigraph ⭐ 367
Proof-of-concept seq-to-graph mapper and graph generator
total releases 1latest release June 21, 2023most recent commit 4 months ago
Nxontology ⭐ 59
NetworkX-based Python library for representing ontologies
dependent packages 2total releases 15latest release February 28, 2023most recent commit 9 months agopypi nxontology} Downloads
Dgl Lifesci ⭐ 558
Python package for graph neural networks in chemistry and biology
dependent packages 4total releases 17latest release December 21, 2022most recent commit a year agopypi dgllife} Downloads
Spacegraphcats ⭐ 112
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
total releases 15latest release December 04, 2022most recent commit 3 months ago
Metage2metabo ⭐ 42
From annotated genomes to metabolic screening in large scale microbiotas
total releases 33latest release September 26, 2022most recent commit 3 months ago
React Cytoscapejs ⭐ 407
React component for Cytoscape.js network visualisations
dependent packages 34total releases 7latest release September 02, 2022most recent commit a year agonpm react-cytoscapejs} Downloads
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