Reed College Computational Biology

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32 repositories

protein-weaver
Public
A web interface for ontology-based protein network visualization.
neo4j gene-ontology web-tool cytoscapejs protein-protein-interaction network-biology
JavaScript
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GNU General Public License v3.0
•5•2•26•8•Updated Dec 9, 2024Dec 9, 2024
spras
Public
Signaling Pathway Reconstruction Analysis Streamliner (SPRAS)
snakemake network omics workkflow
Python
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MIT License
•20•11•86•12•Updated Dec 5, 2024Dec 5, 2024
BowTieBuilder-Algorithm
Public
This repository contains an implementation of the BowTieBuilder Algorithm.
Jupyter Notebook
•2•0•3•0•Updated Dec 4, 2024Dec 4, 2024
protein-function-prediction
Public
A tool to predict protein functions (Gene Ontology) via protein-protein and ontology networks
gene-ontology protein-protein-interaction
Python
•0•1•2•0•Updated Oct 9, 2024Oct 9, 2024
spras-benchmarking
Public
Benchmarking datasets for the SPRAS project
Jupyter Notebook
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MIT License
•5•0•0•5•Updated Sep 22, 2024Sep 22, 2024
ResponseNet
Public
Implementation of the ResponseNet algorithm
Python
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GNU General Public License v3.0
•0•0•0•0•Updated Aug 26, 2024Aug 26, 2024
github-tutorial
Public
0•0•0•0•Updated Jun 6, 2024Jun 6, 2024
growing-dags
Public
Python
•0•0•0•0•Updated Sep 11, 2023Sep 11, 2023
nmii-contractility-regulators
Public
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Sep 5, 2023Sep 5, 2023
random-walk-with-restart
Public
Jupyter Notebook
•
MIT License
•0•0•0•0•Updated Aug 17, 2023Aug 17, 2023
graphlet-clustering
Public
Jupyter Notebook
•
GNU General Public License v3.0
•0•1•0•0•Updated Aug 6, 2023Aug 6, 2023
TieDIE
Public
Tied Diffusion for Subnetwork Discovery (TieDIE)
Python
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Other
•22•0•0•0•Updated Jun 21, 2023Jun 21, 2023
Graphery
Public
A graph tutorial website
website django vue graph-algorithms computational-biology
Python
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MIT License
•3•9•34•21•Updated Mar 5, 2023Mar 5, 2023
pathway-reconciliation
Public
Python
•
GNU General Public License v3.0
•0•2•0•0•Updated Oct 6, 2022Oct 6, 2022
GrapheryV2-Vue
Public
The frontend of Graphery, a graph algorithm tutorial & visualization website
TypeScript
•0•0•0•0•Updated Aug 2, 2022Aug 2, 2022
GrapheryV2-Django
Public
The backend of Graphery, a graph algorithm tutorial & visualization website
Python
•0•0•0•0•Updated Jul 31, 2022Jul 31, 2022
GrapheryExecutor
Public
Graphery Executor
Python
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MIT License
•0•0•0•0•Updated Jul 31, 2022Jul 31, 2022
GrapheryRFCs
Public
MIT License
•0•0•0•0•Updated Jul 28, 2022Jul 28, 2022
networkx
Public
Graphery networkx Wrapper
Python
•
Other
•3.3k•0•0•0•Updated Jun 22, 2022Jun 22, 2022
BIO331-F20
Public
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Aug 25, 2021Aug 25, 2021
BIO331-Datasets
Public
Bio331 Fall 2020 -- Datasets
GNU General Public License v3.0
•0•1•0•0•Updated Aug 25, 2021Aug 25, 2021
pathway-parsers
Public
Signaling pathway database parsers
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Jul 20, 2021Jul 20, 2021
BIO331-F20-Lab6.2-community-detection
Public archive
Bio331 -- Fall 2020 -- Lab 6 Part 2
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Oct 13, 2020Oct 13, 2020
BIO331-F20-Lab6.1-GitHub
Public archive
Bio331 -- Fall 2020-- Lab 6 Part 1
GNU General Public License v3.0
•0•0•0•0•Updated Oct 13, 2020Oct 13, 2020
BIO331-F20-M3-betweenness-centralities
Public archive
Bio331 Fall 2020 -- Module 3
Python
•
GNU General Public License v3.0
•0•0•0•2•Updated Oct 7, 2020Oct 7, 2020
BIO331-F20-Lab5-random-walk-sim
Public archive
Bio331 Fall 2020 -- Lab 5
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Oct 5, 2020Oct 5, 2020
BIO331-F20-Lab4-steiner-tree-approx
Public archive
Biol330 Fall 2020 -- Lab 4
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Sep 29, 2020Sep 29, 2020
BIO331-F20-M2-interactome-properties
Public archive
Bio331 Fall 2020 -- Module 2
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Sep 23, 2020Sep 23, 2020
BIO331-F20-Lab3-shortest-paths
Public archive
Bio331 Fall 2020 -- Module 2 -- Lab 3
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Sep 15, 2020Sep 15, 2020
BIO331-F20-Lab2-animal-network-viz
Public archive
Bio331 Fall 2020 -- Module 1 -- Lab 2
Python
•
GNU General Public License v3.0
•0•0•0•0•Updated Sep 8, 2020Sep 8, 2020