Biomedical Informatics Group

All

27 repositories

cadmus
Public
A full-text article retrieval pipeline for biomedical literature.
information-retrieval corpus-generator bionlp biomedical-text-mining python text-mining
Python
•
MIT License
•2•20•3•0•Updated Nov 4, 2024Nov 4, 2024
biomedicalinformaticsgroup.github.io
Public
Biomedical Informatics Group @informatics, Edinburgh University
HTML
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MIT License
•0•0•0•0•Updated Sep 10, 2024Sep 10, 2024
MOGDxBook
Public
Jupyter Notebook
•0•0•0•0•Updated Jul 22, 2024Jul 22, 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.
chip-seq atac-seq high-throughput-sequencing bioinformatics rna-seq
Python
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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
MOGDx
Public
R
•1•1•0•0•Updated Jan 21, 2024Jan 21, 2024
ParallelPyMetaMap
Public
This code is to run MetaMap in parallel using Python.
python named-entity-recognition bionlp metamap biomedical-text-mining
Python
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MIT License
•0•8•2•0•Updated Jul 20, 2023Jul 20, 2023
oa_pmc_extr
Public
This repository automatically requests and extracts Full Text from Open Access PMC.
Python
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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 biomedical-text-mining pubmed-abstracts
Python
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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
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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/10.1101/2022.03.26.485918v1
1•0•0•0•Updated Mar 28, 2022Mar 28, 2022
gene2phenotype
Public
General repository for gene2phenotype oriented code
Jupyter Notebook
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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
•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
R
•0•0•0•0•Updated May 18, 2021May 18, 2021
meetings
Public
collections of links, notes and materials associated with our joint Bioinformatics meetings
HTML
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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 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 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
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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
miRNAtap.db
Public
R
•0•0•0•0•Updated Aug 20, 2014Aug 20, 2014
targetPredictorUpdater
Public
R
•0•0•0•0•Updated Aug 6, 2014Aug 6, 2014
targetPredictor
Public
project1
R
•0•1•0•0•Updated Aug 6, 2014Aug 6, 2014