neurogenomics

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84 repositories

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•1•0•0•Updated Dec 19, 2024Dec 19, 2024
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
•1•1•4•1•Updated Dec 19, 2024Dec 19, 2024
KGExplorer
Public
Import and analyse large-scale biomedical knowledge graphs and ontologies. 🕸️⚙️💻⚙️🕸️
api bioinformatics big-data knowledge-graph network-analysis biomedicine
R
•1•0•1•1•Updated Dec 19, 2024Dec 19, 2024
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•4•1•1•Updated Dec 19, 2024Dec 19, 2024
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
•7•75•32•0•Updated Dec 18, 2024Dec 18, 2024
neurogenomics-lab-website
Public
Website for the Skene Lab
lab-website neurogenomics
TeX
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MIT License
•4•3•0•0•Updated Dec 12, 2024Dec 12, 2024
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
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•11•0•0•Updated Nov 21, 2024Nov 21, 2024
gpt_hpo_annotations
Public
🏥🧑‍⚕️✨🤖✨👨‍⚕️🏥
JavaScript
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GNU General Public License v3.0
•0•1•1•0•Updated Nov 15, 2024Nov 15, 2024
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•6•5•0•Updated Nov 10, 2024Nov 10, 2024
APOE_microglia
Public
HTML
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GNU General Public License v3.0
•0•0•0•0•Updated Oct 25, 2024Oct 25, 2024
Power_Analysis_package
Public
Repo to wrap "scRNA-seq_Power_Analysis" work into an R package
R
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Other
•0•0•0•0•Updated Oct 22, 2024Oct 22, 2024
EpiCompare
Public
Comparison, benchmarking & QC of epigenetic datasets
html benchmarking benchmark genetics comparison epigenetics bioconductor r-package bioconductor-package interactive-reporting
HTML
•3•13•12•0•Updated Oct 18, 2024Oct 18, 2024
MAGMA_Celltyping
Public
Find causal cell-types underlying complex trait genetics
gwas snps genomics statistical-genetics magma single-cell-omics single-cell
R
•31•74•11•0•Updated Oct 4, 2024Oct 4, 2024
scNLP
Public
Tools for applying natural language processing (NLP) techniques to single-cell (sc) omics data.
Python
•0•0•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•0•7•0•Updated Oct 2, 2024Oct 2, 2024
phenomix
Public
Explore the phenome ✨🎆✨
gwas genomics dimensionality-reduction phenomics decomposition-algorithm
Jupyter Notebook
•0•0•11•0•Updated Oct 2, 2024Oct 2, 2024
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•11•5•1•Updated Oct 2, 2024Oct 2, 2024
Rare-Disease-Web-Portal
Public
Website for the rare disease project
Python
•1•0•0•0•Updated Sep 9, 2024Sep 9, 2024
read1_peak_calling
Public
R
•0•0•0•0•Updated Aug 29, 2024Aug 29, 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
•15•1•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•1•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•1•0•0•Updated Jun 13, 2024Jun 13, 2024
ConsensusPeak
Public
R
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GNU General Public License v3.0
•0•0•6•0•Updated Mar 21, 2024Mar 21, 2024
RareDiseasePrioritisation
Public
Prioritise cell-type-specific gene targets from the Rare Disease Celltyping project.
genomics scrna-seq clinical-research single-cell-genomics aav rare-disease celltypes
HTML
•0•1•0•0•Updated Mar 21, 2024Mar 21, 2024
Kayaking
Public
Kotlin
•0•5•23•0•Updated Mar 12, 2024Mar 12, 2024
labwiki
Public
Tips, intros, and documentation for the Neurogenomics Lab. 🧠 🧬
documentation wiki collaboration knowledge-management
0•8•11•0•Updated Feb 23, 2024Feb 23, 2024
scFlow
Public
Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.
R
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Other
•14•3•0•0•Updated Feb 21, 2024Feb 21, 2024
rare_disease_celltyping_apps
Public
All apps and homepage code in one place for the rare disease EWCE project.
CSS
•1•1•2•0•Updated Jan 27, 2024Jan 27, 2024