Neurogenomics Lab

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87 repositories

gpt_hpo_annotations
Public
🏥🧑‍⚕️✨🤖✨👨‍⚕️🏥
JavaScript
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GNU General Public License v3.0
•0•2•0•0•Updated Sep 10, 2025Sep 10, 2025
neurogenomics-lab-website
Public
Website for the Skene Lab
lab-website neurogenomics
TeX
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MIT License
•3•3•0•0•Updated Sep 8, 2025Sep 8, 2025
MotifPeeker
Public
Benchmark Epigenomic Profiling Methods with Motif Enrichment as Key Metric
bioconductor chip-seq r-package epigenomics bioconductor-package motif-enrichment-analysis interactive-report
R
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GNU General Public License v3.0
•0•2•2•0•Updated Aug 31, 2025Aug 31, 2025
rworkflows
Public
Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳.
docker continuous-integration containers bioconductor dockerhub reproducibility workflows cran-r r github-actions
HTML
•8•81•32•0•Updated Aug 23, 2025Aug 23, 2025
rare_disease_celltyping
Public
Code, data and results associated with the "Rare diseases cell-typing" project.
genetics enrichment-analysis rare-disease cell-type-deconvolution
HTML
•0•8•4•0•Updated Aug 14, 2025Aug 14, 2025
MSTExplorer
Public
Multi-Scale Target Explorer systematically identifies, prioritises, and visualises cell-type-specific gene therapy targets across the phenome.
genetics parallel-computing r-package enrichment-analysis human-phenotype-ontology rare-disease biomedicine cell-types
R
•2•2•3•0•Updated Aug 8, 2025Aug 8, 2025
phenomix.core
Public
Core functions for the phenomix R package
R
•0•0•0•0•Updated Aug 3, 2025Aug 3, 2025
templateR
Public template
Self-updating template for developing R packages.
documentation r templates bioconductor r-package cran-r github-actions
R
•1•5•0•0•Updated Aug 3, 2025Aug 3, 2025
KGExplorer
Public
Import and analyse large-scale biomedical knowledge graphs and ontologies. 🕸️⚙️💻⚙️🕸️
api bioinformatics big-data knowledge-graph network-analysis biomedicine
R
•1•1•1•0•Updated Aug 2, 2025Aug 2, 2025
Power_Analysis_package
Public
Repo to wrap "scRNA-seq_Power_Analysis" work into an R package
R
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Other
•0•2•0•0•Updated Jul 13, 2025Jul 13, 2025
EnformerCelltyping
Public
Enformer Celltyping is a tensorflow, multi-headed attention based model that incorporates distal effects of Deoxyribonucleic Acid (DNA) interactions to predict histone marks across diverse cell types.
Jupyter Notebook
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MIT License
•0•14•0•0•Updated Jun 25, 2025Jun 25, 2025
tf-analysis-cuttag
Public
nanoCUT&TAG analysis of 17 transcription factors (TFs) in K562 human cells
epigenomics motif-enrichment-analysis r-analysis
R
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MIT License
•0•0•0•0•Updated Jun 16, 2025Jun 16, 2025
Rare-Disease-Web-Portal
Public
A web portal for rare disease research with bidirectional queries, integrated datasets, and interactive visualizations for exploring phenotypes, genes, and cell types.
website genetics full-stack enrichment-analysis human-phenotype-ontology rare-disease cell-types
JavaScript
•1•2•16•0•Updated May 7, 2025May 7, 2025
Kayaking
Public
Kotlin
•0•6•23•0•Updated Apr 30, 2025Apr 30, 2025
HPOExplorer
Public
Functions for working with the Human Phenotype Ontology data
bioinformatics genetics r-package ontologies phenome human-phenotype-ontology rare-disease clinical-genomics
R
•1•7•0•0•Updated Mar 11, 2025Mar 11, 2025
orthogene
Public
🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃‍♀️
bioinformatics r genomics bioconductor genes comparative-genomics r-package ontologies evolutionary-biology bioconductor-package
R
•4•45•12•0•Updated Mar 9, 2025Mar 9, 2025
scKirby
Public
Automated ingestion and conversion of various single-cell data formats, within and across species
format-converter standardization single-cell-rna-seq r r-package
R
•2•12•5•0•Updated Mar 9, 2025Mar 9, 2025
MAGMA_Celltyping
Public
Find causal cell-types underlying complex trait genetics
gwas snps genomics statistical-genetics magma single-cell-omics single-cell
R
•32•91•11•0•Updated Feb 25, 2025Feb 25, 2025
EpiCompare
Public
Comparison, benchmarking & QC of epigenetic datasets
html benchmarking benchmark genetics comparison epigenetics bioconductor r-package bioconductor-package interactive-reporting
HTML
•3•17•13•0•Updated Feb 16, 2025Feb 16, 2025
EvoCT_coding
Public
R
•0•1•1•0•Updated Jan 6, 2025Jan 6, 2025
MotifPeeker-reports
Public
Public archive of reports generated using MotifPeeker R package
r database reproducible-research epigenomics
HTML
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GNU General Public License v3.0
•0•0•0•0•Updated Dec 2, 2024Dec 2, 2024
scNLP
Public
Tools for applying natural language processing (NLP) techniques to single-cell (sc) omics data.
Python
•0•1•0•0•Updated Oct 2, 2024Oct 2, 2024
PeakyFinders
Public
R package for mining, calling, and importing epigenomic peaks.
genomics encode epigenomics gene-expression-omnibus peak-calling r r-package
R
•0•1•7•0•Updated Oct 2, 2024Oct 2, 2024
phenomix
Public
Explore the phenome ✨🎆✨
gwas genomics dimensionality-reduction phenomics decomposition-algorithm
Jupyter Notebook
•0•1•11•0•Updated Oct 2, 2024Oct 2, 2024
read1_peak_calling
Public
R
•0•0•0•0•Updated Aug 29, 2024Aug 29, 2024
Az_MAGMA_Benchmarking
Public
This is a repo for my MAGMA benchmarking project with Imperial
R
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GNU General Public License v3.0
•1•0•0•0•Updated Aug 28, 2024Aug 28, 2024
peak_calling_tutorial
Public
HTML
•0•0•0•0•Updated Aug 16, 2024Aug 16, 2024
MungeSumstats
Public
Rapid standardisation and quality control of GWAS or QTL summary statistics
R
•18•3•0•0•Updated Aug 7, 2024Aug 7, 2024
chromexpress
Public
Which epigenetic factors are the best predictors of gene expression? An analysis using ENCODE data.
Python
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MIT License
•1•4•0•0•Updated Jul 25, 2024Jul 25, 2024
MotifStats
Public
Package for integrating peak and motif positions
R
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GNU General Public License v3.0
•1•2•0•0•Updated Jun 13, 2024Jun 13, 2024