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Search results for graph bioinformatics
bioinformatics
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graph
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42 search results found
Graphein
⭐
932
Protein Graph Library
Dgl Lifesci
⭐
558
Python package for graph neural networks in chemistry and biology
Grakel
⭐
540
A scikit-learn compatible library for graph kernels
Hifiasm
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443
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
React Cytoscapejs
⭐
407
React component for Cytoscape.js network visualisations
Minigraph
⭐
367
Proof-of-concept seq-to-graph mapper and graph generator
Canvasxpress
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282
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
Ppanggolin
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191
Build a partitioned pangenome graph from microbial genomes
Gfatools
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181
Tools for manipulating sequence graphs in the GFA and rGFA formats
Graphtyper
⭐
156
Population-scale genotyping using pangenome graphs
Ontobio
⭐
114
python library for working with ontologies and ontology associations
Bio4j
⭐
112
Bio4j abstract model and general entry point to the project
Spacegraphcats
⭐
112
Indexing & querying large assembly graphs -- in space, no one can hear you miao!
Tutorial
⭐
94
Tutorials on machine learning, artificial intelligence, data science with math explanation and reusable code (in python and R)
Bcalm
⭐
90
compacted de Bruijn graph construction in low memory
Pybel
⭐
89
🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)
Arcs
⭐
86
🌈Scaffold genome sequence assemblies using linked or long read sequencing data
Pygr
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84
Python graph database framework for bioinformatics
Fermi Lite
⭐
67
Standalone C library for assembling Illumina short reads in small regions
Gatb Core
⭐
61
Core library of the Genome Analysis Toolbox with de-Bruijn graph
Nxontology
⭐
59
NetworkX-based Python library for representing ontologies
Gbwt
⭐
55
Substring index for paths in a graph
Graph Network Explainability
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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)
Raptor
⭐
50
Graph-based mapping of long sequences, noisy or HiFi.
Biokeen
⭐
43
A computational library for learning and evaluating biological knowledge graph embeddings - please see the main PyKEEN repo at https://github.com/pykeen/pykeen/
Metage2metabo
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42
From annotated genomes to metabolic screening in large scale microbiotas
Gfapy
⭐
39
Gfapy: a flexible and extensible software library for handling sequence graphs in Python
Twopaco
⭐
39
A fast constructor of the compressed de Bruijn graph from many genomes
Synthetic
⭐
37
Symbolic Generators for Complex Networks
Genomegraphs.jl
⭐
29
A modern genomics framework for julia
Stratipy
⭐
29
Graph regularized nonnegative matrix factorization (GNMF) in Python
Covid19kg
⭐
27
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology
Grafimo
⭐
22
GRAph-based Finding of Individual Motif Occurrences
Metagenomescope
⭐
22
Visualization tool for (meta)genome assembly graphs
Gedfn
⭐
19
GEDFN: Graph-Embedded Deep Feedforward Network
Metacherchant
⭐
19
Correlationplus
⭐
18
A Python package to calculate, visualize and analyze correlation maps of proteins.
Goo
⭐
15
Graph Oriented Objects (GOO) for Ruby. A RDF/SPARQL based ORM.
Clep
⭐
13
🤖 A Python Package for generating new patient representations driven by data and prior knowledge
Cbioinfcpp 0
⭐
12
The lib CBioInfCpp.h contains 3 groups of functions for C++: "Input-Output", "Working with strings", "Working with graphs". Data structures "Adjacency vector" and "Adjacency map" are implemented in the last one (i.e. in "Working with graphs"). See About_CBioInfCpp for details.
Genomics Workspace
⭐
11
Django website project for common sequence search tools.
Algebra
⭐
10
A Boolean Algebra for Genetic Variants
Acad18
⭐
10
Day 2 of ACAD's 2018 Advanced Bioinformatics Workshop
Biodwh2
⭐
10
BioDWH2 is an easy-to-use, automated, graph-based data warehouse and mapping tool for bioinformatics and medical informatics.
Kleuren
⭐
8
Find bubbles in the Colored de Bruijn Graph to reconstruct phylogenetic trees
Bifusion
⭐
7
Goetia
⭐
6
Streaming de Bruijn and Compact de Bruijn Graph Algorithms
Bovine Graphs
⭐
6
Integrate multiple genome assemblies into a pangenome graph
Canvasxpress Js
⭐
6
CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.
Awesome Ai
⭐
5
Awesome list for all things AI, ML and deep learning
Recon2neo4j
⭐
5
This framework is part of the DiseaseNetworks module, eTRIKS Lab. The Metabolic Framework uses the neo4j graph platform for the management of data on human metabolism (basis: Recon2).
Pathway2vec
⭐
5
Leveraging Heterogeneous Network Embedding for Metabolic Pathway Prediction
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1-42 of 42 search results
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