neurogenomics

MotifPeeker

Benchmark Epigenomic Profiling Methods with Motif Enrichment as Key Metric

EnformerCelltyping

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.

rworkflows

Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳.

APOE_microglia

chromexpress

Which epigenetic factors are the best predictors of gene expression? An analysis using ENCODE data.

rare_disease_celltyping

Code, data and results associated with the "Rare diseases cell-typing" project.

MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics

HPOExplorer

Functions for working with the Human Phenotype Ontology data

MotifPeeker-reports

Public archive of reports generated using MotifPeeker R package

scKirby

Automated ingestion and conversion of various single-cell data formats, within and across species

MotifStats

Package for integrating peak and motif positions

KGExplorer

Import and analyse large-scale biomedical knowledge graphs and ontologies. 🕸️⚙️💻⚙️🕸️

gpt_hpo_annotations

🏥🧑‍⚕️✨🤖✨👨‍⚕️🏥

neurogenomics-lab-website

MAGMA_Celltyping

Find causal cell-types underlying complex trait genetics

MSTExplorer

Multi-Scale Target Explorer systematically identifies, prioritises, and visualises cell-type-specific gene therapy targets across the phenome.

EpiCompare

Comparison, benchmarking & QC of epigenetic datasets

ConsensusPeak

RareDiseasePrioritisation

Prioritise cell-type-specific gene targets from the Rare Disease Celltyping project.

Kayaking

labwiki

Tips, intros, and documentation for the Neurogenomics Lab. :brain: 🧬

scFlow

Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.

rare_disease_celltyping_apps

All apps and homepage code in one place for the rare disease EWCE project.

Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

orthogene

🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃‍♀️

GenomicRanges

Representation and manipulation of genomic intervals

.github

Neurogenomics Lab Profile

templateR

Self-updating template for developing R packages.

reanalysis_Mathys_2019

A re-analysis of the [Single-cell transcriptomic analysis of Alzheimer’s disease](https://www.nature.com/articles/s41586-019-1195-2) using a standardised data processing and pseudobulk differential expression approach

ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)