neurogenomics/labwiki

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neurogenomics/labwiki

neurogenomics

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Tips, intros, and documentation for the Neurogenomics Lab. 🧠 🧬

MAGMA_Celltyping

Find causal cell-types underlying complex trait genetics

rworkflows

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

MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics

orthogene

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

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

EpiCompare

Comparison, benchmarking & QC of epigenetic datasets

scKirby

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

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.

Jupyter Notebook

Kayaking

templateR

Self-updating template for developing R packages.

TERRA_Tutorial

Guide to creating very simple WDL workflows and pushing them to TERRA via dockstore

rare_disease_celltyping

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

CHAS

Cell type-specific Histone Acetylation Score

MAGMA_Files_Public

Publicly shared SNP-to-gene mappings of GWAS generated by MAGMA.

scFlowExamples

HPOExplorer

Functions for working with the Human Phenotype Ontology data

NextFlowIntro

neurogenomics-lab-website

MotifPeeker

Benchmark Epigenomic Profiling Methods with Motif Enrichment as Key Metric

document_and_share

Strategies for documentation and sharing of data analyses.

MotifStats

Package for integrating peak and motif positions

rare_disease_celltyping_apps

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

RareDiseasePrioritisation

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

MSTExplorer

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

EpiPrepare

Preprocessing of epigenomic data from fastq files.

EWCE