https://github.com/jackhump/als_spinalcord_qtls
Data Portal for NYGC ALS Spinal Cord
https://github.com/jackhump/als_spinalcord_qtls
Last synced: 5 months ago
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Data Portal for NYGC ALS Spinal Cord
- Host: GitHub
- URL: https://github.com/jackhump/als_spinalcord_qtls
- Owner: jackhump
- Created: 2021-08-24T15:34:53.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2023-08-30T17:58:28.000Z (almost 3 years ago)
- Last Synced: 2023-08-31T06:36:00.370Z (almost 3 years ago)
- Language: HTML
- Homepage:
- Size: 23.8 MB
- Stars: 3
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
## ALS Spinal Cord differential expression and molecular QTLs
Jack Humphrey 2019-2023
## Manuscript
[Publication in Nature Neuroscience](https://www.nature.com/articles/s41593-022-01205-3)
[Link to preprint on medrxiv](https://www.medrxiv.org/content/10.1101/2021.08.31.21262682v1)
## Shiny App
[Launch Shiny app](https://rstudio-connect.hpc.mssm.edu/als_spinal_cord_browser/)
[source code](https://github.com/jackhump/ALS_SpinalCord_QTLs/blob/master/als_spinal_cord_browser/app.R)
## Data Availability
[Raw RNA-seq data - Gene Expression Omnibus](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137810)
[Processed gene expression count matrices with de-identified metadata - Zenodo](https://zenodo.org/record/6385747)
[An HTML vignette on downloading the count data from Zenodo and performing differential expression](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/DE_Vignette.html)
Whole genome sequencing data - dbGAP (in progress).
[Full summary statistics for expression and splicing QTLs - Zenodo](https://zenodo.org/record/5248758).
[All TWAS weight files - Zenodo](https://zenodo.org/record/5256613)
[All marker genes used](https://github.com/jackhump/ALS_SpinalCord_QTLs/tree/master/markers)
## Rmarkdown workbooks written for the project.
Workbooks are available as [RMarkdown files](https://github.com/jackhump/ALS_SpinalCord_QTLs/tree/master/scripts). Knitted HTMLs can be browsed with the links below.
### Data QC and setup
[RNA-seq QC](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_covariates_setup.html)
WGS QC pipeline hosted [here](https://github.com/jackhump/WGS-QC-Pipeline)
[Building sets of marker genes](https://github.com/jackhump/ALS_SpinalCord_QTLs/blob/master/scripts/ALS_marker_lists.Rmd)
All marker sets are shared as RData objects [here](https://github.com/jackhump/ALS_SpinalCord_QTLs/tree/master/markers)
### Differential expression
[Running differential expression](https://github.com/jackhump/ALS_SpinalCord_QTLs/blob/master/scripts/ALS_differential_expression.Rmd)
[Volcano plots, GSEA, marker gene overlaps](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_deg_functions.html)
[Cell-type deconvolution](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_deconvolution.html)
### Co-expression networks
[Building co-expression networks, associations with traits and GO](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_WGCNA.html)
### Quantitative Trait Loci (QTLs)
[QTL results per region and sharing with GTEx](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_QTL_results.html)
[Colocalisation with ALS GWAS](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_COLOC.html)
[Transcriptome-wide association study - TWAS](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_TWAS.html)
### Gene prioritisation
[C9orf72 and ATXN3](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ATXN3_C9orf72.html)
[Transcript plots](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_locus_plots.html)
[Localising genes to cell-types](https://jackhump.github.io/ALS_SpinalCord_QTLs/html/ALS_genes_celltypes.html)