All

33 repositories

gnn-suite
Public
Nextflow pipeline to train several GNN architectures
Jupyter Notebook
•4•3•0•0•Updated Apr 21, 2026Apr 21, 2026
biomedicalinformaticsgroup.github.io
Public
Biomedical Informatics Group @Informatics, Edinburgh University
HTML
•
MIT License
•0•0•0•0•Updated Mar 27, 2026Mar 27, 2026
LitDD_mining
Public
Map peer-reviewed literature for genetic disease and extract data
Python
•
MIT License
•1•1•1•0•Updated Dec 1, 2025Dec 1, 2025
cadmus_methods_extraction
Public
A lightweight standalone tool for extracting the Methods section from biomedical full-text articles.
Python
•
MIT License
•0•1•0•0•Updated Nov 25, 2025Nov 25, 2025
ParallelPyMetaMap
Public
This code is to run MetaMap in parallel using Python.
python named-entity-recognition bionlp
python named-entity-recognition bionlp metamap biomedical-text-mining
Python
•
MIT License
•0•8•1•0•Updated Nov 25, 2025Nov 25, 2025
cadmus
Public
A full-text article retrieval pipeline for biomedical literature.
python information-retrieval text-mining
python information-retrieval text-mining corpus-generator bionlp biomedical-text-mining
Python
•
MIT License
•2•23•1•0•Updated Nov 24, 2025Nov 24, 2025
MOGDx
Public
Jupyter Notebook
•2•0•0•0•Updated Aug 6, 2025Aug 6, 2025
bioasq2025
Public
Group submission for bioASQ 2025
Jupyter Notebook
•1•0•0•0•Updated May 12, 2025May 12, 2025
MOGDxBook
Public
Jupyter Notebook
•0•0•0•0•Updated Feb 5, 2025Feb 5, 2025
MOLLM
Public
Jupyter Notebook
•0•0•0•0•Updated Jan 28, 2025Jan 28, 2025
asd_stratification_with_psn
Public
Jupyter Notebook
•1•0•0•0•Updated Nov 26, 2024Nov 26, 2024
networks_ismb24
Public
Jupyter Book for the Networks Tutorial at ISMB2024, Montreal, Canada.
Jupyter Notebook
•1•2•1•0•Updated Jul 16, 2024Jul 16, 2024
Sargasso
Public
Sargasso disambiguates mixed-species high-throughput sequencing data.
bioinformatics rna-seq chip-seq
bioinformatics rna-seq chip-seq atac-seq high-throughput-sequencing
Python
•
Other
•4•8•11•0•Updated Feb 6, 2024Feb 6, 2024
MOGDx-PPMI
Public
R
•0•1•0•0•Updated Jan 21, 2024Jan 21, 2024
oa_pmc_extr
Public
This repository automatically requests and extracts Full Text from Open Access PMC.
Python
•
MIT License
•0•1•1•0•Updated May 30, 2023May 30, 2023
pm_abs_extr
Public
This repository automatically requests and extracts abstract from PubMed.
python text-mining bionlp
python text-mining bionlp biomedical-text-mining pubmed-abstracts
Python
•
MIT License
•0•1•1•0•Updated May 28, 2023May 28, 2023
bionlp_resources
Public
Repository where we can keep scripts related to other projects
Python
•
MIT License
•0•1•0•0•Updated May 27, 2023May 27, 2023
rb_vs_ode_model_of_darpp-32
Public
Repository storing molecular rule-based models in Kappa language and Python-based figures published as the BioRxiv preprint: https://www.biorxiv.org/content/10.…
1•0•0•0•Updated Mar 28, 2022Mar 28, 2022
gene2phenotype
Public
General repository for gene2phenotype oriented code
Jupyter Notebook
•
MIT License
•1•0•0•1•Updated Mar 8, 2022Mar 8, 2022
clusterCons
Public
Merged consensus clustering to assess and improve class discovery with microarray data
r clustering
r clustering
R
•0•1•0•0•Updated Feb 22, 2022Feb 22, 2022
sfariexpression
Public
Code repository for SFARI Genes and where to find them; classification modelling to identify genes associated with Autism Spectrum Disorder from RNA-seq data
disease gene-expression-signatures autism-spectrum-disorder
disease gene-expression-signatures autism-spectrum-disorder
R
•1•0•0•0•Updated May 18, 2021May 18, 2021
meetings
Public
collections of links, notes and materials associated with our joint Bioinformatics meetings
HTML
•
MIT License
•3•0•0•0•Updated Jun 10, 2019Jun 10, 2019
ddp2neo4j
Public
developmental disorders phenotype
Python
•0•0•1•0•Updated Dec 5, 2018Dec 5, 2018
statbio.github.io
Public
HTML
•0•0•1•0•Updated Sep 27, 2018Sep 27, 2018
topOnto
Public
topOnto - An R package for generically enabled ontology enrichment analysis
bioinformatics r ontology
bioinformatics r ontology sea enrichment-analysis
R
•2•2•0•0•Updated Jun 27, 2017Jun 27, 2017
OntoSuite-Miner
Public
An NLP pipeline for annotating ontologies from biomedical corpora
natural-language-processing bioinformatics database
natural-language-processing bioinformatics database ontology biomedical-text-mining
Perl
•1•0•0•0•Updated Jun 27, 2017Jun 27, 2017
PPI_RDF
Public
Python
•1•0•0•0•Updated Jan 8, 2016Jan 8, 2016
topOnto.HDO.db
Public
ontology package for human disease ontology
Perl
•0•0•0•0•Updated Oct 9, 2015Oct 9, 2015
piquant
Public
A pipeline to assess the quantification of transcripts
Python
•
MIT License
•4•0•0•0•Updated Oct 2, 2015Oct 2, 2015
miRNAtap
Public
R
•0•0•0•0•Updated Aug 22, 2014Aug 22, 2014

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Biomedical Informatics Group

All

All

33 repositories

gnn-suite

biomedicalinformaticsgroup.github.io

LitDD_mining

cadmus_methods_extraction

ParallelPyMetaMap

cadmus

MOGDx

bioasq2025

MOGDxBook

MOLLM

asd_stratification_with_psn

networks_ismb24

Sargasso

MOGDx-PPMI

oa_pmc_extr

pm_abs_extr

bionlp_resources

rb_vs_ode_model_of_darpp-32

gene2phenotype

clusterCons

sfariexpression

meetings

ddp2neo4j

statbio.github.io

topOnto

OntoSuite-Miner

PPI_RDF

topOnto.HDO.db

piquant

miRNAtap

All

All

Repositories list

33 repositories