ALS_SpinalCord_QTLs
ALS Spinal Cord differential expression and molecular QTLs
Jack Humphrey 2019-2023
Manuscript
Publication in Nature Neuroscience
Shiny App
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
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
WGS QC pipeline hosted here
All marker sets are shared as RData objects here
Differential expression
Running differential expression
Volcano plots, GSEA, marker gene overlaps
Co-expression networks
Building co-expression networks, associations with traits and GO
Quantitative Trait Loci (QTLs)
QTL results per region and sharing with GTEx
Transcriptome-wide association study - TWAS