Biomedical Informatics Group

cadmus

A full-text article retrieval pipeline for biomedical literature.

ParallelPyMetaMap

This code is to run MetaMap in parallel using Python.

Sargasso

Sargasso disambiguates mixed-species high-throughput sequencing data.

topOnto

topOnto - An R package for generically enabled ontology enrichment analysis

bionlp_resources

Repository where we can keep scripts related to other projects

clusterCons

Merged consensus clustering to assess and improve class discovery with microarray data

oa_pmc_extr

This repository automatically requests and extracts Full Text from Open Access PMC.

pm_abs_extr

This repository automatically requests and extracts abstract from PubMed.

targetPredictor

project1

biomedicalinformaticsgroup.github.io

Biomedical Informatics Group @Informatics, Edinburgh University

ddp2neo4j

developmental disorders phenotype

gene2phenotype

General repository for gene2phenotype oriented code

meetings

collections of links, notes and materials associated with our joint Bioinformatics meetings

MOGDx

MOGDx-PPMI

OntoSuite-Miner

An NLP pipeline for annotating ontologies from biomedical corpora

PPI_RDF

sfariexpression

Code repository for SFARI Genes and where to find them; classification modelling to identify genes associated with Autism Spectrum Disorder from RNA-seq data

statbio.github.io

miRNAtap

miRNAtap.db

piquant

A pipeline to assess the quantification of transcripts

rb_vs_ode_model_of_darpp-32

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

targetPredictorUpdater

topOnto.HDO.db

ontology package for human disease ontology