/ALS_SpinalCord_QTLs

Data Portal for NYGC ALS Spinal Cord

Primary LanguageHTML

ALS Spinal Cord differential expression and molecular QTLs

Jack Humphrey 2019-2023

deg figure

Manuscript

Publication in Nature Neuroscience

Link to preprint on medrxiv

Shiny App

Launch Shiny app

source code

Data Availability

Raw RNA-seq data - Gene Expression Omnibus

Processed gene expression count matrices with de-identified metadata - Zenodo

An HTML vignette on downloading the count data from Zenodo and performing differential expression

Whole genome sequencing data - dbGAP (in progress).

Full summary statistics for expression and splicing QTLs - Zenodo.

All TWAS weight files - Zenodo

All marker genes used

Rmarkdown workbooks written for the project.

Workbooks are available as RMarkdown files. Knitted HTMLs can be browsed with the links below.

Data QC and setup

RNA-seq QC

WGS QC pipeline hosted here

Building sets of marker genes

All marker sets are shared as RData objects here

Differential expression

Running differential expression

Volcano plots, GSEA, marker gene overlaps

Cell-type deconvolution

Co-expression networks

Building co-expression networks, associations with traits and GO

Quantitative Trait Loci (QTLs)

QTL results per region and sharing with GTEx

Colocalisation with ALS GWAS

Transcriptome-wide association study - TWAS

Gene prioritisation

C9orf72 and ATXN3

Transcript plots

Localising genes to cell-types